Ramachandran plot in ISOLDE (libbz2.so.1.0 not found)

[luigi@…]

Hi, 

I'm trying to visualize the Ramachandran plot for my structure in ISOLDE but I'm getting the following error message:




ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory

File "/raid/1/software/chimerax/0.6/lib/python3.6/bz2.py", line 23, in 
from _bz2 import BZ2Compressor, BZ2Decompressor

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.




Colud you please help me?




Thanks, 





Luigi


Luigi De Colibus, PhD
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
 

-----Original Message-----
From: "Tristan Croll" <tic20@cam.ac.uk>
To: "Luigi De Colibus" <luigi@strubi.ox.ac.uk>
Date: 06/05/18 18:02
Subject: Re: Re[2]: Help with ISOLDE

Hi Luigi,

My guess is that you have one or more cysteine residues with truncated sidechains. While ISOLDE will accept most residues truncated to Ala or Gly, Cys is the one current exception. The reason for that boils down to the fact that I need to tell the MD library what each cysteine is, since otherwise it can't tell the difference between one that's deprotonated and one that is disulfide bonded but has the other Cys missing from the simulation. When writing the code for that, I neglected to consider truncated residues. Build in your cysteine sidechains and you should be fine.


Cheers,


Tristan


 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 


 

On 5 Jun 2018, at 17:54, Luigi De Colibus <luigi@strubi.ox.ac.uk> wrote:




Dear Tristan,





I'm trying to refine and rebuild my structure with ISOLDE, but I Get the following error message:



Exception: User-supplied template CYM does not match the residue 34 (CYS)

File "/raid/1/software/chimerax/0.6/lib/python3.6/site-packages/simtk/openmm/app/forcefield.py", line 1054, in createSystem
raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name))

See log for complete Python traceback.





I checked in my PDB file, and there is no residue named CYM.





Could you please advice me on how to fix this problem?





Thanks,





Luigi




Luigi De Colibus, PhD
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
 

-----Original Message-----
From: "Tristan Croll" <tic20@cam.ac.uk>
To: "Luigi De Colibus" <luigi@strubi.ox.ac.uk>
Cc: "Jun Dong" <jun@strubi.ox.ac.uk>
Date: 05/17/18 12:04
Subject: Re: Help with ISOLDE

Hi Luigi,

As such things go, the video tutorial is already somewhat out of date. If you click the "Help" button in the top right of the ISOLDE panel, you'll find some quite comprehensive and current html documentation.


As for your specific issue: you need to load the map(s) first using the "Add map(s) from MTZ" button. I'll make this clearer in the next release.


Best regards,


Tristan


 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 


 

On 17 May 2018, at 10:40, Luigi De Colibus <luigi@strubi.ox.ac.uk> wrote:




Dear Dr Troll,





my name is Luigi De Colibus, and I'm a postdoc at the Division of Structural Biology of Oxford University.





I'm writing you because I'd like the run ISOLDE on my low-resolution cryo-EM structure through ChimeraX but when I click on the button :
" Show map settings dialogue"





I get the following error message:




AttributeError: 'NoneType' object has no attribute 'child_models'

File "/raid/1/software/chimerax/0.6/lib/python3.6/site-packages/chimerax/clipper/symmetry.py", line 132, in get_symmetry_handler
for m in structure.child_models():

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.







Could you please help me to fix this issue?





Moreover,I'm also looking the ISOLDE tutorial on youTUBE and some of the options available in the version employed to run the tutorial don't seem to be present anymore  in the version I got in ChimeraX.
I'm wondering if there is an updated version of the tutorial.

Thanks a lot in advance for your help!





Best Regards,





Luigi




Luigi De Colibus, PhD
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
 

[tic20@…]

This is sorted out (Luigi emailed me directly). It's an issue with the 
bzip2 package for CentOS 7: it has libbz2.so, libbz2.so.1, 
libbz2.so.1.0.6, but not libbz2.so.1.0. Go figure. The workaround is to 
simply create the missing symlink. The library itself is being called by 
Matplotlib.

On 2018-06-12 17:02, ChimeraX wrote:

[Greg Couch]

matplotlib doesn't refer to libbz anymore.