error during structure calculation

[tlamer]

Hi there,

I am trying to use xplor3.8 to calculate a structure but I am getting an error that I am not sure how to fix. Analysis seems to be able to find xplor and talos, but then seems to be unable to find a certain database. The error is:

Summarizing Phi/Psi Predictions …
Summarizing Chi1 Predictions …
Running time: 70.0774 seconds
Spectrum Name Num Peaks
nef_nmr_spectrum_600Nhsqc-NOESY1 541
nef_nmr_spectrum_800cnoesy1 411

dyld[21147]: Library not loaded: libxplorCmd.dylib
Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.8/bin.Darwin/xplor

I am not sure what path to check for this library but it seems that the program can’t seem to find it.

Any insights would be greatly appreciated :)

[varioustoxins]

Hi

1. this looks like the xplor installation is not correct, did you run ./configure?

2. libxplorCmd.dylib should be in ./bin.Darwin/xlibs/libxplorCmd.dylib can you check its there it should be about 190k in size if its not then reinstall

3. what sort of Mac are you running? intel or MX? do you have the right executables if its a newer Mac?

4. If these don’t help reinstall from scratch and then if the problem persists contact Charles on the xplor nah mailing list he is very helpful and obviously very knowledgeable

regards
Gary

[ElizaP]

Hi,

Current version of Analysis v3 is not yet compatible with Xplor NIH 3.8.

Do you have 2d data in your set?

I can try to finalise the update, but it will be tomorrow soonest.

Regards,
Eliza

[tlamer]

Hi Gary and Eliza,

Thanks so much- I will download an older version of xplor instead of 3.8, as that is likely the issue here. I had ran the configure command and can see the libxplorCmd.dylib in the location you indicated Gary (looks like it is 190 k so should be downloaded correctly). And yes I have a couple of 2D spectra and several 3D.

Thanks!!

[ElizaP]

Hi,

If you have 2d NOESY then you have to use Xplor Nih 3.8.

Current tutorial is set up for Xplor Nih version 3.5, that is what I would recommend. Make sure you set up your symbolic links for xplor on your machine (instructions are in INSTALL Xplor distribution).

Any questions let us know.
Eliza

[tlamer]

Hi there,

We have downloaded xplor 3.5 and are still getting similar errors. I will just paste below the entire output because I’m not really sure what it is supposed to look like. It is ignoring chemical shifts of all atoms assigned so I’m not sure if that is an error or not.

[Johns-MacBook-Pro:data/xplor_nih/run-2-2024-05-09-104242] johnvederas% ./script.sh

nefShifts: reading table: default

nefShifts: ignoring shift entry with residue id 2-1

nefShifts: ignoring shift entry with residue id 2-1

nefShifts: ignoring shift entry with residue id 2-1

nefShifts: ignoring shift entry with residue id 3-1

nefShifts: ignoring shift entry with residue id 3-1

nefShifts: ignoring shift entry with residue id 4-1

nefShifts: ignoring shift entry with residue id 4-1

nefShifts: ignoring shift entry with residue id 4-1

nefShifts: ignoring shift entry with residue id 5-1

nefShifts: ignoring shift entry with residue id 5-1

nefShifts: ignoring shift entry with residue id 5-1

nefShifts: ignoring shift entry with residue id 6-1

nefShifts: ignoring shift entry with residue id 6-1

nefShifts: ignoring shift entry with residue id 6-1

nefShifts: ignoring shift entry with residue id 7-1

nefShifts: ignoring shift entry with residue id 7-1

nefShifts: ignoring shift entry with residue id 7-1

nefShifts: ignoring shift entry with residue id 8-1

nefShifts: ignoring shift entry with residue id 8-1

nefShifts: ignoring shift entry with residue id 8-1

nefShifts: ignoring shift entry with residue id 9-1

nefShifts: ignoring shift entry with residue id 9-1

nefShifts: ignoring shift entry with residue id 9-1

nefShifts: ignoring shift entry with residue id 9-1

nefShifts: ignoring shift entry with residue id 9-1

nefShifts: ignoring shift entry with residue id 10-1

nefShifts: ignoring shift entry with residue id 10-1

nefShifts: ignoring shift entry with residue id 10-1

nefShifts: ignoring shift entry with residue id 11-1

nefShifts: ignoring shift entry with residue id 11-1

nefShifts: ignoring shift entry with residue id 11-1

nefShifts: ignoring shift entry with residue id 12-1

nefShifts: ignoring shift entry with residue id 12-1

nefShifts: ignoring shift entry with residue id 13-1

nefShifts: ignoring shift entry with residue id 13-1

nefShifts: ignoring shift entry with residue id 13-1

nefShifts: ignoring shift entry with residue id 14-1

nefShifts: ignoring shift entry with residue id 14-1

nefShifts: ignoring shift entry with residue id 15-1

nefShifts: ignoring shift entry with residue id 15-1

nefShifts: ignoring shift entry with residue id 15-1

nefShifts: ignoring shift entry with residue id 17-1

nefShifts: ignoring shift entry with residue id 17-1

nefShifts: ignoring shift entry with residue id 17-1

nefShifts: ignoring shift entry with residue id 18-1

nefShifts: ignoring shift entry with residue id 18-1

nefShifts: ignoring shift entry with residue id 18-1

nefShifts: ignoring shift entry with residue id 19-1

nefShifts: ignoring shift entry with residue id 19-1

nefShifts: ignoring shift entry with residue id 20-1

nefShifts: ignoring shift entry with residue id 20-1

nefShifts: ignoring shift entry with residue id 20-1

nefShifts: ignoring shift entry with residue id 21-1

nefShifts: ignoring shift entry with residue id 21-1

nefShifts: ignoring shift entry with residue id 21-1

nefShifts: ignoring shift entry with residue id 22-1

nefShifts: ignoring shift entry with residue id 22-1

nefShifts: ignoring shift entry with residue id 22-1

nefShifts: ignoring shift entry with residue id 23-1

nefShifts: ignoring shift entry with residue id 23-1

nefShifts: ignoring shift entry with residue id 23-1

nefShifts: ignoring shift entry with residue id 24-1

nefShifts: ignoring shift entry with residue id 24-1

nefShifts: ignoring shift entry with residue id 24-1

nefShifts: ignoring shift entry with residue id 25-1

nefShifts: ignoring shift entry with residue id 25-1

nefShifts: ignoring shift entry with residue id 25-1

nefShifts: ignoring shift entry with residue id 26-1

nefShifts: ignoring shift entry with residue id 26-1

nefShifts: ignoring shift entry with residue id 26-1

nefShifts: ignoring shift entry with residue id 27-1

nefShifts: ignoring shift entry with residue id 27-1

nefShifts: ignoring shift entry with residue id 27-1

nefShifts: ignoring shift entry with residue id 28-1

nefShifts: ignoring shift entry with residue id 28-1

nefShifts: ignoring shift entry with residue id 28-1

nefShifts: ignoring shift entry with residue id 29-1

nefShifts: ignoring shift entry with residue id 29-1

nefShifts: ignoring shift entry with residue id 29-1

nefShifts: ignoring shift entry with residue id 30-1

nefShifts: ignoring shift entry with residue id 30-1

nefShifts: ignoring shift entry with residue id 30-1

nefShifts: ignoring shift entry with residue id 31-1

nefShifts: ignoring shift entry with residue id 31-1

nefShifts: ignoring shift entry with residue id 32-1

nefShifts: ignoring shift entry with residue id 32-1

nefShifts: ignoring shift entry with residue id 32-1

nefShifts: ignoring shift entry with residue id 34-1

nefShifts: ignoring shift entry with residue id 34-1

nefShifts: ignoring shift entry with residue id 34-1

nefShifts: ignoring shift entry with residue id 35-1

nefShifts: ignoring shift entry with residue id 35-1

nefShifts: ignoring shift entry with residue id 35-1

nefShifts: ignoring shift entry with residue id 36-1

nefShifts: ignoring shift entry with residue id 36-1

nefShifts: ignoring shift entry with residue id 36-1

nefShifts: ignoring shift entry with residue id 42-1

nefShifts: ignoring shift entry with residue id 42-1

nefShifts: ignoring shift entry with residue id 42-1

nefShifts: ignoring shift entry with residue id 43-1

nefShifts: ignoring shift entry with residue id 43-1

nefShifts: ignoring shift entry with residue id 43-1

nefShifts: ignoring shift entry with residue id 44-1

nefShifts: ignoring shift entry with residue id 44-1

nefShifts: ignoring shift entry with residue id 44-1

nefShifts: ignoring shift entry with residue id 45-1

nefShifts: ignoring shift entry with residue id 45-1

nefShifts: ignoring shift entry with residue id 45-1

nefShifts: ignoring shift entry with residue id 46-1

nefShifts: ignoring shift entry with residue id 46-1

nefShifts: ignoring shift entry with residue id 47-1

nefShifts: ignoring shift entry with residue id 47-1

nefShifts: ignoring shift entry with residue id 47-1

nefShifts: ignoring shift entry with residue id 48-1

nefShifts: ignoring shift entry with residue id 48-1

nefShifts: ignoring shift entry with residue id 48-1

nefShifts: ignoring shift entry with residue id 49-1

nefShifts: ignoring shift entry with residue id 49-1

nefShifts: ignoring shift entry with residue id 49-1

nefShifts: ignoring shift entry with residue id 50-1

nefShifts: ignoring shift entry with residue id 50-1

nefShifts: ignoring shift entry with residue id 50-1

nefShifts: ignoring shift entry with residue id 51-1

nefShifts: ignoring shift entry with residue id 51-1

nefShifts: ignoring shift entry with residue id 51-1

nefShifts: ignoring shift entry with residue id 52-1

nefShifts: ignoring shift entry with residue id 52-1

nefShifts: ignoring shift entry with residue id 52-1

nefShifts: ignoring shift entry with residue id 53-1

nefShifts: ignoring shift entry with residue id 53-1

nefShifts: ignoring shift entry with residue id 53-1

nefShifts: ignoring shift entry with residue id 54-1

nefShifts: ignoring shift entry with residue id 54-1

nefShifts: ignoring shift entry with residue id 54-1

nefShifts: ignoring shift entry with residue id 55-1

nefShifts: ignoring shift entry with residue id 55-1

nefShifts: ignoring shift entry with residue id 55-1

nefShifts: ignoring shift entry with residue id 56-1

nefShifts: ignoring shift entry with residue id 56-1

nefShifts: ignoring shift entry with residue id 56-1

nefShifts: ignoring shift entry with residue id 57-1

nefShifts: ignoring shift entry with residue id 57-1

nefShifts: ignoring shift entry with residue id 57-1

nefShifts: ignoring shift entry with residue id 58-1

nefShifts: ignoring shift entry with residue id 58-1

nefShifts: ignoring shift entry with residue id 58-1

nefShifts: ignoring shift entry with residue id 59-1

nefShifts: ignoring shift entry with residue id 59-1

nefShifts: ignoring shift entry with residue id 59-1

nefShifts: ignoring shift entry with residue id 60-1

nefShifts: ignoring shift entry with residue id 60-1

nefShifts: ignoring shift entry with residue id 60-1

nefShifts: ignoring shift entry with residue id 61-1

nefShifts: ignoring shift entry with residue id 61-1

nefShifts: ignoring shift entry with residue id 61-1

nefShifts: ignoring shift entry with residue id 62-1

nefShifts: ignoring shift entry with residue id 62-1

nefShifts: ignoring shift entry with residue id 62-1

nefShifts: ignoring shift entry with residue id 63-1

nefShifts: ignoring shift entry with residue id 63-1

nefShifts: ignoring shift entry with residue id 64-1

nefShifts: ignoring shift entry with residue id 64-1

nefShifts: ignoring shift entry with residue id 64-1

nefShifts: ignoring shift entry with residue id 66-1

nefShifts: ignoring shift entry with residue id 66-1

nefShifts: ignoring shift entry with residue id 66-1

nefShifts: ignoring shift entry with residue id 67-1

nefShifts: ignoring shift entry with residue id 67-1

nefShifts: ignoring shift entry with residue id 67-1

nefShifts: ignoring shift entry with residue id 68-1

nefShifts: ignoring shift entry with residue id 68-1

nefShifts: ignoring shift entry with residue id 68-1

nefShifts: ignoring shift entry with residue id 69-1

nefShifts: ignoring shift entry with residue id 69-1

nefShifts: ignoring shift entry with residue id 69-1

nefShifts: ignoring shift entry with residue id 70-1

nefShifts: ignoring shift entry with residue id 70-1

nefShifts: ignoring shift entry with residue id 70-1

nefShifts: ignoring shift entry with residue id 71-1

nefShifts: ignoring shift entry with residue id 71-1

nefShifts: ignoring shift entry with residue id 71-1

nefShifts: ignoring shift entry with residue id 72-1

nefShifts: ignoring shift entry with residue id 72-1

nefShifts: ignoring shift entry with residue id 72-1

nefShifts: ignoring shift entry with residue id 73-1

nefShifts: ignoring shift entry with residue id 73-1

nefShifts: ignoring shift entry with residue id 73-1

nefShifts: ignoring shift entry with residue id 74-1

nefShifts: ignoring shift entry with residue id 74-1

nefShifts: ignoring shift entry with residue id 74-1

nefShifts: ignoring shift entry with residue id 75-1

nefShifts: ignoring shift entry with residue id 75-1

nefShifts: ignoring shift entry with residue id 75-1

nefShifts: ignoring shift entry with residue id 76-1

nefShifts: ignoring shift entry with residue id 76-1

nefShifts: ignoring shift entry with residue id 76-1

nefShifts: ignoring shift entry with residue id 77-1

nefShifts: ignoring shift entry with residue id 77-1

nefShifts: ignoring shift entry with residue id 77-1

nefShifts: ignoring shift entry with residue id 78-1

nefShifts: ignoring shift entry with residue id 78-1

nefShifts: ignoring shift entry with residue id 78-1

nefShifts: ignoring shift entry with residue id 79-1

nefShifts: ignoring shift entry with residue id 79-1

nefShifts: ignoring shift entry with residue id 80-1

nefShifts: ignoring shift entry with residue id 80-1

nefShifts: ignoring shift entry with residue id 80-1

nefShifts: ignoring shift entry with residue id 81-1

nefShifts: ignoring shift entry with residue id 81-1

nefShifts: ignoring shift entry with residue id 81-1

nefShifts: ignoring shift entry with residue id 82-1

nefShifts: ignoring shift entry with residue id 82-1

nefShifts: ignoring shift entry with residue id 82-1

nefShifts: ignoring shift entry with residue id 83-1

nefShifts: ignoring shift entry with residue id 83-1

nefShifts: ignoring shift entry with residue id 83-1

nefShifts: ignoring shift entry with residue id 84-1

nefShifts: ignoring shift entry with residue id 84-1

nefShifts: ignoring shift entry with residue id 84-1

nefShifts: ignoring shift entry with residue id 85-1

nefShifts: ignoring shift entry with residue id 85-1

nefShifts: ignoring shift entry with residue id 85-1

nefShifts: ignoring shift entry with residue id 86-1

nefShifts: ignoring shift entry with residue id 86-1

nefShifts: ignoring shift entry with residue id 86-1

nefShifts: ignoring shift entry with residue id 87-1

nefShifts: ignoring shift entry with residue id 87-1

nefShifts: ignoring shift entry with residue id 87-1

nefShifts: ignoring shift entry with residue id 88-1

nefShifts: ignoring shift entry with residue id 88-1

nefShifts: ignoring shift entry with residue id 88-1

nefShifts: ignoring shift entry with residue id 89-1

nefShifts: ignoring shift entry with residue id 89-1

nefShifts: ignoring shift entry with residue id 89-1

nefShifts: ignoring shift entry with residue id 90-1

nefShifts: ignoring shift entry with residue id 91-1

nefShifts: ignoring shift entry with residue id 91-1

nefShifts: ignoring shift entry with residue id 92-1

nefShifts: ignoring shift entry with residue id 92-1

nefShifts: ignoring shift entry with residue id 92-1

nefShifts: ignoring shift entry with residue id 93-1

nefShifts: ignoring shift entry with residue id 93-1

nefShifts: ignoring shift entry with residue id 93-1

nefShifts: ignoring shift entry with residue id 94-1

nefShifts: ignoring shift entry with residue id 94-1

nefShifts: ignoring shift entry with residue id 95-1

nefShifts: ignoring shift entry with residue id 95-1

nefShifts: ignoring shift entry with residue id 95-1

nefShifts: ignoring shift entry with residue id 96-1

nefShifts: ignoring shift entry with residue id 96-1

nefShifts: ignoring shift entry with residue id 96-1

nefShifts: ignoring shift entry with residue id 97-1

nefShifts: ignoring shift entry with residue id 97-1

nefShifts: ignoring shift entry with residue id 97-1

nefShifts: ignoring shift entry with residue id 98-1

nefShifts: ignoring shift entry with residue id 98-1

nefShifts: ignoring shift entry with residue id 100-1

nefShifts: ignoring shift entry with residue id 100-1

nefShifts: ignoring shift entry with residue id 100-1

nefShifts: ignoring shift entry with residue id 101-1

nefShifts: ignoring shift entry with residue id 101-1

nefShifts: ignoring shift entry with residue id 101-1

nefShifts: ignoring shift entry with residue id 102-1

nefShifts: ignoring shift entry with residue id 102-1

nefShifts: ignoring shift entry with residue id 102-1

nefShifts: ignoring shift entry with residue id 103-1

nefShifts: ignoring shift entry with residue id 103-1

nefShifts: ignoring shift entry with residue id 103-1

nefShifts: ignoring shift entry with residue id 104-1

nefShifts: ignoring shift entry with residue id 104-1

nefShifts: ignoring shift entry with residue id 104-1

nefShifts: ignoring shift entry with residue id 105-1

nefShifts: ignoring shift entry with residue id 105-1

nefShifts: ignoring shift entry with residue id 105-1

nefShifts: ignoring shift entry with residue id 106-1

nefShifts: ignoring shift entry with residue id 106-1

nefShifts: ignoring shift entry with residue id 106-1

nefShifts: ignoring shift entry with residue id 107-1

nefShifts: ignoring shift entry with residue id 107-1

nefShifts: ignoring shift entry with residue id 107-1

nefShifts: ignoring shift entry with residue id 108-1

nefShifts: ignoring shift entry with residue id 108-1

nefShifts: ignoring shift entry with residue id 108-1

nefShifts: ignoring shift entry with residue id 109-1

nefShifts: ignoring shift entry with residue id 109-1

nefShifts: ignoring shift entry with residue id 109-1

nefShifts: ignoring shift entry with residue id 110-1

nefShifts: ignoring shift entry with residue id 110-1

nefShifts: ignoring shift entry with residue id 110-1

nefShifts: ignoring shift entry with residue id 111-1

nefShifts: ignoring shift entry with residue id 111-1

nefShifts: ignoring shift entry with residue id 111-1

nefShifts: ignoring shift entry with residue id 112-1

nefShifts: ignoring shift entry with residue id 112-1

nefShifts: ignoring shift entry with residue id 112-1

nefShifts: ignoring shift entry with residue id 113-1

nefShifts: ignoring shift entry with residue id 113-1

nefShifts: ignoring shift entry with residue id 113-1

nefShifts: ignoring shift entry with residue id 114-1

nefShifts: ignoring shift entry with residue id 114-1

nefShifts: ignoring shift entry with residue id 114-1

nefShifts: ignoring shift entry with residue id 115-1

nefShifts: ignoring shift entry with residue id 115-1

nefShifts: ignoring shift entry with residue id 115-1

nefShifts: ignoring shift entry with residue id 116-1

nefShifts: ignoring shift entry with residue id 116-1

nefShifts: ignoring shift entry with residue id 116-1

nefShifts: ignoring shift entry with residue id 117-1

nefShifts: ignoring shift entry with residue id 117-1

nefShifts: ignoring shift entry with residue id 117-1

nefShifts: ignoring shift entry with residue id 118-1

nefShifts: ignoring shift entry with residue id 118-1

nefShifts: ignoring shift entry with residue id 118-1

nefShifts: ignoring shift entry with residue id 119-1

nefShifts: ignoring shift entry with residue id 119-1

1018 shifts were read from NEF data.

Traceback (most recent call last):

File “”, line 1, in

File “/opt/xplor-nih-3.5/python/xplorInit.py”, line 137, in execfile

exec(code, globals, locals)

File “./genTalosNInput.py”, line 45, in

raise Exception(“sel: (%s) does not any atoms”%sel)

Exception: sel: (segid A and resid 2 and resname GLY and name HA) does not any atoms

Failed to find an installed nmrPipe system

A stand-alone version TALOS-N installation is used.

The following nmrPipe related features are disabled:

. automatic TALOS/BMRB format input indentication and conversion

. automatic identical database protein identification and exclusion

Testing /opt/bin/TALOSN

Testing /opt/bin/TALOSN.linux9_x64

Testing /opt/bin/TALOSN.linux9

Testing /opt/bin/TALOSN.mac

Testing /opt/bin/TALOSN.static.linux9_x64

Testing /opt/bin/TALOSN.static.linux9

Testing /opt/bin/TALOSN.mac.10.15

Running /opt/bin/TALOSN.mac.10.15 -in input.nef.tab -np 1

--------------------------------------------------------------------

This is the TALOS-N system for predicting protein backbone/sidechain

torsion angles and secondary structure from NMR chemical shifts.

TALOS-N is an enhanced version of the TALOS/TALOS+ systems.

TALOS-N relies more extensively on the artificial neural networks

than TALOS+ and improves upon the original TALOS/TALOS+ by an

optimized database mining scheme. TALOS-N offers additional

predictions for sidechain chi1 rotameric states.

There is also a complementary system, called SPARTA+, which can

predict backbone chemicals shifts from a PDB structure.

For more information, see:

Ad Bax Group Software - Biophysical Nuclear Magnetic Resonance Spectroscopy...

Ad Bax Group Software - Biophysical Nuclear Magnetic Resonance Spectroscopy...

Reference:

Y. Shen, and A. Bax:

Protein backbone and sidechain torsion angles predicted from NMR

chemical shifts using artificial neural networks

J. Biomol. NMR, 56, 227-241(2013).

TALOS-N Version 4.21 Rev 2016.343.11.31 TALOSN_INFO

--------------------------------------------------------------------

Can’t open file input.nef.tab for reading

Traceback (most recent call last):

File “”, line 1, in

File “/opt/xplor-nih-3.5/python/xplorInit.py”, line 137, in execfile

exec(code, globals, locals)

File “./talosToNEF.py”, line 14, in

restraints = convertTalosN(predFile=“pred.tab”,

File “/opt/xplor-nih-3.5/python/talosTools.py”, line 26, in convertTalosN

pred=GDB(predFile)

File “/opt/xplor-nih-3.5/python/wrappers/sparta.py”, line 955, in init

_sparta.GDB_swiginit(self, _sparta.new_GDB(*args))

SystemError: xplor-nih error: GDB::loadGDB: Can’t open file pred.tab for reading.

Spectrum Name Num Peaks

nef_nmr_spectrum_600Nhsqc-NOESY1 541

nef_nmr_spectrum_800cnoesy1 411

dyld[66209]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 49: 66209 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor initMatch3d.py ${name}.nef $spectrum

dyld[66210]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 49: 66210 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor initMatch3d.py ${name}.nef $spectrum

dyld[66211]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 58: 66211 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor jointFilter.py ${name}.nef $spectra

dyld[66212]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 68: 66212 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor -parallel -smp 12 pass2.py ${name}_new.nef $spectra

dyld[66213]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 74: 66213 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor summarize_pass2.py ${name}_new.nef $spectra

dyld[66214]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 82: 66214 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor -parallel -smp 12 pass3.py ${name}_new.nef $spectra

dyld[66215]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 88: 66215 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor summarize_pass3.py ${name}_new.nef $spectra

dyld[66216]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 94: 66216 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor makeNEF.py ${name}_new.nef $spectra

dyld[66217]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 102: 66217 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor -parallel -smp 12 fold.py -nef out.nef

grep: fold_##.sa.stats: No such file or directory

tail: -: No such file or directory

grep: Invalid argument

dyld[66241]: Library not loaded: libxplorCmd.dylib

Referenced from: <3E248E73-20F6-37AA-962A-301D2FC64A87> /opt/xplor-nih-3.5/bin.Darwin/xplor

Reason: tried: ‘libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OSlibxplorCmd.dylib’ (no such file), ‘libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/Users/johnvederas/Downloads/SUMO_structure_May7.ccpn/data/xplor_nih/run-2-2024-05-09-104242/libxplorCmd.dylib’ (no such file), ‘/usr/local/lib/libxplorCmd.dylib’ (no such file), ‘/usr/lib/libxplorCmd.dylib’ (no such file, not in dyld cache)

./script.sh: line 112: 66241 Abort trap: 6 /opt/xplor-nih-3.5/bin.Darwin/xplor -parallel -smp 12 refine.py -nef out.nef $(getBest -num 10 -suffix .cif fold_##.sa.stats)

[Johns-MacBook-Pro:data/xplor_nih/run-2-2024-05-09-104242] johnvederas%

Sorry for the very long message here, just wanted to give you all the information!

Thanks a bunch

Tess

[tlamer]

File was in the correct directory. We tried 3.8, 3.7 and now 3.5. Intel mac with intel executables.
The xplor testDist runs without issue, but when we try to call on Xplor via CCPN …the script.sh falls down with the errors posted below.
Many many thanks

[tlamer]

We have 3D datasets (e.g. 3D-15N-NOESY and 3D-13C-NOESY, etc.) along with 3d assignment experiments such as 3D-HCCH-TOCSY, CBCA(CO)NNH etc.

[VickyH]

I wonder if it is worth trying to run your XPLOR calculation on NMRbox?
There is a list of VMs running XPLOR-NIH 3.5 here:

NMRbox.org

It lookes as though the chemical shifts that are being ignored, are the all the i-1 offset ones - you might want to merge them to the main ones. Have a look at this post for how to do this:

Synthetic peak list and merging i and i-1

Hi Christian, I looked into the merging stuff. This is something which is still rather rudimentary at the moment, but certainly something we will be sorting out in future. The main thing to bear in mind (and I think the reason this wasn’t sorted sooner) is that merging NmrAtoms is irreversible and not undoable. So for this is reason the programme doesn’t do this automatically, and we will certainly always leave this as something that the user has to initiate themselves. So before doing any me…

But do archive your project first before doing this.

Vicky

[ElizaP]

Hi,

You have a line in the traceback (thank you for sending it!):
“Exception: sel: (segid A and resid 2 and resname GLY and name HA) does not any atoms”
That is because there is no HA atom in GLY, in accordance with NEF naming convention you can only have HAx, HAy or HA%. Script will trip on any atom it does not recognise.

Could you check with the projects we provide in tutorials?
structure_2.ccpn is the starting point for calculations, it would be good to exclude any issues with the data.
https://ccpn.le.ac.uk/download/ccpnmr/v3TutorialData/StructureTutorial.zip
It is quite large file.

Which operating system are you using? Is it Mac M1?

Best wishes,
Eliza

[tlamer]

Hi Eliza,

I’ve merged the chemical shifts of i-1 residues as you indicated, and have moved my data file and spectra over to nmrbox. I also tried to clean up atom assignments as you suggested to conform to the naming conventions (there were a couple of errors in my assignments). I opened the structure tutorial files on nmrbox and am running the calculation right now, and it seems to be moving forward as expected (just a bit slow).

For running my files, the set up process seems to go further than it did when I was trying to do it on my computer (Mac intel chip), but it is still not completing a structure calculation or generating any files in the “fold” folder. At the start of the process I do see two errors, which I am not sure how to resolve and may be the issue? It then ends the output with an error in finding .nef file. Please see abbreviated output below:

1004 shifts were read from NEF data.
Traceback (most recent call last):
File “”, line 1, in
File “/usr/software/xplor-nih/python/xplorInit.py”, line 137, in execfile
exec(code, globals, locals)
File “./genTalosNInput.py”, line 61, in
raise Exception(“more than two HA Glycine entries for (%s)?”%
Exception: more than two HA Glycine entries for (segid A and resid 118 and resname GLY and name HA#)?
Using Executable /usr/software/nmrpipe/talosplus/bin/TALOS+.linux9 …
TALOS+ Error Finding Chemical Shift Input.
Traceback (most recent call last):
File “”, line 1, in
File “/usr/software/xplor-nih/python/xplorInit.py”, line 137, in execfile
exec(code, globals, locals)
File “./talosToNEF.py”, line 14, in
restraints = convertTalosN(predFile=“pred.tab”,
File “/usr/software/xplor-nih/python/talosTools.py”, line 26, in convertTalosN
pred=GDB(predFile)
File “/usr/software/xplor-nih/python/wrappers/sparta.py”, line 955, in init
_sparta.GDB_swiginit(self, _sparta.new_GDB(*args))
SystemError: xplor-nih error: GDB::loadGDB: Can’t open file pred.tab for reading.
Spectrum Name Num Peaks
nef_nmr_spectrum_600Nhsqc-NOESY1 541
nef_nmr_spectrum_800cnoesy1 402

…

Traceback (most recent call last):
File “”, line 2, in
File “/usr/software/xplor-nih/python/trace.py”, line 180, in run
exec(cmd, dict, dict)
File “”, line 1, in
File “/usr/software/xplor-nih/python/xplorInit.py”, line 137, in execfile
exec(code, globals, locals)
File “initMatch3d.py”, line 84, in
assignmentInfo=createShiftAssignments(shifts,noePot,
File “/usr/software/xplor-nih/python/trace.py”, line 218, in func_wrapper
trace.suspend()
File “/usr/software/xplor-nih/python/pasd/init.py”, line 1429, in createShiftAssignments
shiftSelectionList.append( (float(val),float(err),sel) )
ValueError: could not convert string to float: '.'
HEAP: maximum use= 2411969 current use= 2364637
X-PLOR: total CPU time= 1.4798 s
X-PLOR: entry time at 22:23:35 13-May-24
X-PLOR: exit time at 22:23:37 13-May-24

…

reading shift assignments from [string] … [0 loaded]
reading peaks from [string] … [0 loaded]
reading exceptions from [string] [0 loaded]
jointFilter.py(42): pot.setUseSingleAssignment(True)
jointFilter.py(43): noes.append(pot)
jointFilter.py(45): pass
jointFilter.py(36): for name in spectrumNames:
jointFilter.py(37): from pasdPotTools import create_PASDPot
jointFilter.py(38): pot=create_PASDPot(name,
jointFilter.py(39): shifts=f"{name}{passName}.shiftAssignments",
jointFilter.py(40): peaks=f"{name}{passName}.peaks",
jointFilter.py(41): exceptions=f"{name}_{passName}.exceptions")
jointFilter.py(38): pot=create_PASDPot(name,

reading shift assignments from [string] … [0 loaded]
reading peaks from [string] … [0 loaded]
reading exceptions from [string] [0 loaded]
jointFilter.py(42): pot.setUseSingleAssignment(True)
jointFilter.py(43): noes.append(pot)
jointFilter.py(45): pass
jointFilter.py(36): for name in spectrumNames:
jointFilter.py(47): from pasd.protocol import jointFilter
jointFilter.py(49): jointFilter(noes,
jointFilter.py(50): assignmentThreshold=20,
jointFilter.py(51): deleteNonIntraPAs=True,
jointFilter.py(52): writeFiles=True)
jointFilter.py(49): jointFilter(noes,
num from/to shift assignments: 0/0
num residPairs: 0
Reading peakAssignments… 0 total
net filter iteration 0 of 5
sumScores: 0.0000000000
intraresScores: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
Iteration 0 of 5: Calculating new peakAssignment scores
Min peak score is -1.000000

Iteration 0: num peaks zeroed 0

num passing: 0
net filter iteration 1 of 5
sumScores: 0.0000000000
intraresScores: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
Iteration 1 of 5: Calculating new peakAssignment scores
Min peak score is -1.000000

Iteration 1: num peaks zeroed 0

num passing: 0
net filter iteration 2 of 5
sumScores: 0.0000000000
intraresScores: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
Iteration 2 of 5: Calculating new peakAssignment scores
Min peak score is -1.000000

Iteration 2: num peaks zeroed 0

num passing: 0
net filter iteration 3 of 5
sumScores: 0.0000000000
intraresScores: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
Iteration 3 of 5: Calculating new peakAssignment scores
Min peak score is -1.000000

Iteration 3: num peaks zeroed 0

num passing: 0
net filter iteration 4 of 5
sumScores: 0.0000000000
intraresScores: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
Iteration 4 of 5: Calculating new peakAssignment scores
Min peak score is -1.000000

Iteration 4: num peaks zeroed 0
num passing: 0
Recording which peakAssignments passed the filter
0 of 14161 (0.00%) residue pairs passed
Creating explicit inverse exceptions for ShiftAssignment pairs
pot: 600Nhsqc-NOESY1 # exceptions: 0
pot: 800cnoesy1 # exceptions: 0
Traceback (most recent call last):
File “”, line 2, in
File “/usr/software/xplor-nih/python/trace.py”, line 180, in run
exec(cmd, dict, dict)
File “”, line 1, in
File “/usr/software/xplor-nih/python/xplorInit.py”, line 137, in execfile
exec(code, globals, locals)
File “jointFilter.py”, line 49, in
jointFilter(noes,
File “/usr/software/xplor-nih/python/pasd/protocol.py”, line 65, in jointFilter
nfResults = netFilter(pots,verbose=2,
File “/usr/software/xplor-nih/python/trace.py”, line 218, in func_wrapper
trace.suspend()
File “/usr/software/xplor-nih/python/pasd/netfilter.py”, line 962, in netFilter
val = 100.0 * float(nExceptionsCreated[pot.instanceName()]) /
ZeroDivisionError: float division by zero
process 58: irregular exit.
process 19: irregular exit.
process 15: irregular exit.
process 9: irregular exit.
process 17: irregular exit.
process 18: irregular exit.
process 43: irregular exit.
process 33: irregular exit.
process 52: irregular exit.
process 11: irregular exit.
process 7: irregular exit.
process 42: irregular exit.
process 56: irregular exit.
process 14: irregular exit.
process 6: irregular exit.
process 27: irregular exit.
process 55: irregular exit.
process 46: irregular exit.
process 23: irregular exit.
process 5: irregular exit.
process 26: irregular exit.
process 45: irregular exit.
process 70: irregular exit.
process 8: irregular exit.
process 47: irregular exit.
process 64: irregular exit.
process 63: irregular exit.
process 44: irregular exit.
process 57: irregular exit.
process 20: irregular exit.
process 35: irregular exit.
process 24: irregular exit.
process 60: irregular exit.
process 39: irregular exit.
process 62: irregular exit.
process 61: irregular exit.
process 4: irregular exit.
process 65: irregular exit.
process 13: irregular exit.
process 22: irregular exit.
process 69: irregular exit.
process 1: irregular exit.
process 67: irregular exit.
process 48: irregular exit.
process 37: irregular exit.
process 32: irregular exit.
process 21: irregular exit.
process 10: irregular exit.
process 40: irregular exit.
process 71: irregular exit.
process 38: irregular exit.
process 25: irregular exit.
process 49: irregular exit.
process 16: irregular exit.
process 54: irregular exit.
process 66: irregular exit.
process 41: irregular exit.
process 2: irregular exit.
process 0: irregular exit.
process 50: irregular exit.
process 3: irregular exit.
process 31: irregular exit.
process 53: irregular exit.
process 30: irregular exit.
process 12: irregular exit.
process 34: irregular exit.
process 28: irregular exit.
process 68: irregular exit.
process 51: irregular exit.
process 36: irregular exit.
process 29: irregular exit.
process 59: irregular exit.

…

summarize_pass2.py(10): from nefTools import readNEF
summarize_pass2.py(11): nef = readNEF(nefFile) # generates PSF information
Traceback (most recent call last):
File “”, line 2, in
File “/usr/software/xplor-nih/python/trace.py”, line 180, in run
exec(cmd, dict, dict)
File “”, line 1, in
File “/usr/software/xplor-nih/python/xplorInit.py”, line 137, in execfile
exec(code, globals, locals)
File “summarize_pass2.py”, line 11, in
nef = readNEF(nefFile) # generates PSF information
File “/usr/software/xplor-nih/python/nefTools.py”, line 34, in readNEF
dataString=open(filenameOrString).read()
FileNotFoundError: [Errno 2] No such file or directory: 'input_new.nef’

Thanks a lot for your help!

Tess

[VickyH]

Hi Tess,

glad things are working out better on NMRbox.

It looks like there is still a problem with at least one Glycine:

@tlamer

raise Exception(“more than two HA Glycine entries for (%s)?”%
Exception: more than two HA Glycine entries for (segid A and resid 118 and resname GLY and name HA#)?

I wonder if this is stopping the correct chemical shift file from being written for TALOS and then the rest of the errors just start piling up.

In terms of your Glycine HAs: if you can see peaks at two distinct chemical shifts, then you should name these HAx and HAy (i.e. the chemical shifts are not degenerate, but you can’t make a stereospecific assignment). If you only see one chemical shift, then you should use HA% (i.e. the two HA chemical shifts are degenerate and so any peaks contain information about both HAs). Note that HA% in NEF format will get changed to HA# in XPLOR/TALOS format. Might you accidentally have both an HAx and an HA% for Gly 118? Sometimes you do get situations where the HAx and HAy chemical shifts are quite close and so you can distinguish them in some spectra, but in others (with lower resolution) you can’t. In that situation you should make sure that the combined peak is labelled as being assigned to both HAx and HAy, rather than HA%. You shouldn’t ever have a situation where you have HAx, HAy and HA% for a single residue - it should always be either HAx and HAy OR HA%.

Hope that will help you sort things out.

Vicky