Running structure calculation errors

Analysis Version 3
#1

Hi thanks for the help with the fits.

Making the volumes same as the heights allowed me to run the setup xplor_nih structure calculation module.

This creates a directory with several files including a nef file with my sequence, chemical shifts and my picked NOESY peaks. It all seems to look good. Assign structure then says run script.sh. Oh and my TALOS and xplor nih is set up and say success for external programs when tested.

The errors are due to python files that do not exist that I guess should be in the package. There’s like 20 errors. But all of the same type. Please find examples here.

Analyzing Chemical Shifts …
A full amino acid sequence is required in the DATA SEQUENCE header, exit …
./runTalos.sh: line 25: ./talosToNEF.py: No such file or directory
Spectrum Name Num Peaks
Traceback (most recent call last):
File “”, line 4, in
NameError: name ‘getBlockNames’ is not defined
PyInterp::command: error executing: >from nefTools import *
nef = readNEF(‘input.nef’)
print("%25s %6s" % (“Spectrum Name”, “Num Peaks”))
for n in getBlockNames(nef, ‘spectrum’):
print("%25s %6d" %(n, len(getBlock(nef,‘spectrum’,n).nef_peak.index)))

<e “/usr/local/src/SOURCES/xplor-nih-2.53/python/trace.py”, line 180, in run
exec cmd in dict, dict
File “”, line 1, in
IOError: [Errno 2] No such file or directory: ‘initMatch3d.py’
PyInterp::command: error executing: >execfile(‘initMatch3d.py’)<
HEAP: maximum use= 628650 current use= 616818
X-PLOR: total CPU time= 0.0404 s
X-PLOR: entry time at 16:29:52 3-May-24
X-PLOR: exit time at 16:29:52 3-May-24

#2

Hi Joe

which version of xplor are you running?

regards
Gary

#3

xplor 3.6.1. which version is currently optimised for assign v3?

also as per the first error, talos can not run as the talostoNEF.py fails

thanks,

Joe

#4

Hi Joe,

Your error trace says you are using xplor-nih-2.53 version:

I am not entirely sure what is happening there to be honest, if version xplor-nih-3.6.1 is set in your preferences. Maybe there is an issue with symbolic links to ‘xplor’? (In Xplor NIH distribution there is an INSTALL file with instructions how to do it.)

I would recommend downloading Xplor NIH version 3.5, for which current tutorial is written. I will try to add a warning message to the pop-up.

The reason why you are getting all those errors is that scripts expects certain files to be copied from Xplor NIH distribution, which do not exist in xplor-nih-2.53 version.

Kind regards,
Eliza

#5

Good spot. I maybe set the wrong path. Let me try again.

Same with TALOS I guess. Not sure which version I need.

Thanks,

Joe

#6

In terms of TALOS you will simply need to let XPLOR run this (it comes packaged, I think - @ElizaP ?). At the moment you can’t run TALOS itself directly from a NEF file.

Vicky

#7

That is correct, the only way at the moment to run Talos from NEF file is through Xplor-NIH, I have: ‘TALOS-N Version 4.21’ installed on my machine, which I think is the latest.
Path to Talos executable is set in scripts (copied from your preferences) and Xplor NIH ‘translates’ shifts in NEF format for Talos and subsequently turns the result back to NEF format.

Eliza

#8

You can also use pipelines to output to talos input files and read the results back in… and this is supported standalone

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:phone::01227 82 7117
:email:: g.s.thompson@kent.ac.uk
orchid: ORCID

#9

Let me know if you need a tutorial but hopefully it should be obvious

regards
Gary

Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ

:phone::01227 82 7117
:email:: g.s.thompson@kent.ac.uk
orchid: ORCID

#10

In the odd case where there is no error for a value, it breaks. But I check now and the latest version of xplor fixes the set up so all the python files are in the xplor directory now.

nefShifts: reading table: default
1459 shifts were read from NEF data.
Traceback (most recent call last):
File “”, line 1, in
File “./genTalosNInput.py”, line 42, in
for (val,sel,err) in shifts:
ValueError: need more than 2 values to unpack
PyInterp::command: error executing: >execfile(’./genTalosNInput.py’)<
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 /usr/local/src/SOURCES/talosn/bin/TALOSN
Testing /usr/local/src/SOURCES/talosn/bin/TALOSN.linux9_x64
Running /usr/local/src/SOURCES/talosn/bin/TALOSN.linux9_x64 -in input.nef.tab -np 1

in a minor number of cases, there is no error for a value especially if one can only find a weak peak in one spectra. I guess this is breaking the script, because all others have 3 values.

Thanks.

#11

Hi Joe,

Would it be possible to send us your entire xplor nih calculation folder (support@ccpn.ac.uk)? This would be the easiest way to troubleshoot. If not, can you please send me your script that is generated during set up.

Sorry you are having so many issues, I would very much like to know how to sort this out.

Best wishes,
Eliza

#12

One more thing that might be an issue - do you have any chemical shifts that have no error?
Eliza

#13

Yes there are a few. I’ll send the xplor nih calculation folder to support@ccpn.ac.uk.

Thanks,

Joe

#14

a couple of other things to look out for

  1. you will want to inspect the results of the TALOS analysis, it gets it wrong some times (not its fault, its a good program, its just inherent in the statistical analysis). So we always went with areas with determined secondary structure and 2-3 or more consistent TALOS results in alpha or bea space the first time and then added more as justified
  2. some programs draw the TALOS XPLOR restraints very tight, this may not be what you want…

regards
Gary