Issues with ChemBuild


I`m trying to make a modified Cysteine residue (Cys with a maleimido-prenyl covalently attached to the SG). 

I insert the residue using a SMILE string and then want to modify labels, make it a biopolymer (by setting the link points for the peptide bonds) and eventually obviously want to export this to be used in a CCPN project.

However, everytime I either save the molecule and re-open it, and more importantly when I try to carry out actions like setting atoms as residue links, the molecule just disappears and I`m left with just the labels. 

I was wondering how I can fix this or if it`s a known bug?



Dear Sam, Thank you for reporting this issue. Just found and fixed the bug, we shall send to the updates shortly. Keep the saved files as you will be able to open them back as normal.

From experience, I`ve found that it`s more reliable to start with an existing amino acid that is as close as possible to your non-natural or modified one and build on the extra parts. This way, the majority of linking info & ionization states are already the way you want them.



I am wondering if this bug has been fixed yet for the Mac version or if there is a workaround? I am having the same issue currently when trying to generate a small peptide with modified residues. I`ve found this also happens if you try and undo something. You can continue adding new atoms/residues from the left panel and they will appear fine, but I can`t find any way of making existing atoms or molecules reappear.


Hi, an update for ChemBuild is now available. This has fixed the issue with redrawing lines after undoing or exporting.

Hi Luca,

That bug is sorted. The next problem I`ve had is with the export function. I`m trying to export the molecule to a CCPN XML file and got the following error:

Traceback (most recent call last):
  File `/Applications/`, line 1133, in exportChemComp
    stream = open(streamPath, `w`)
FileNotFoundError: [Errno 2] No such file or directory: `/Users/Sam/Desktop/MF1/protein+MF1+ChemBuild_Sam_2020-02-11-18-50-00-029_00001.xml`

The program seems to be trying to find a directory in which to save the file, while the export menu says `save file as`. I actually managed to get round this issue by sending it to someone using the Beta2 release where the export function works with no issue. I thought I would mention on here to bring it to your/others attention.



Thanks, Sam. This is the same as the issue that @ThomasK posted the other day.
I posted quite a long reply in that which may be of interest to you:

Best wishes,