[Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models

Wed Dec 6 06:37:13 PST 2017

P.S. is it possible to make a complex task script for batch chimera
e.g to find contacts between all of the chains and other atoms in the
sequential manner adding the results within the same log?

# an example of such workflow within one batch input file for the batch chimera
findclash :.a test other overlapCutoff -3.0 intraMol false saveFile
./test_cont.log
findclash :.b test other overlapCutoff -3.0 intraMol false saveFile
./test_cont.log
...
findclash :.p test other overlapCutoff -3.0 intraMol false saveFile
./test_cont.log

2017-12-06 15:02 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> Elaine,
>
> the question was related not to the bash script for this routine but
> instead to the input file for the batch chimera.
>
> E.g. I have indentified the following command which works in command
> line of Chimera GUI. It finds the contacts between chain A and others
> and save the outputs to the log file in the same dir.
>
> findclash :.a test other overlapCutoff -3.0 intraMol false saveFile
> ./test_cont.log
>
> Now when I had put the same line into the input.batch and executed it
> with the batch_chimera, i have recieved the following error message
> from python:
>
> chimera_batch ./rep2.pdb ./xz.batch
> Opening rep2.pdb..
> Traceback (most recent call last):
>   File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimeraInit.py",
> line 708, in init
>     chimera.openModels.open(a, prefixableType=1)
>   File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
> line 1916, in open
>     raise ValueError, "Unknown model type"
> ValueError: Unknown model type
>
> Error while processing ./xz.batch:
> ValueError: Unknown model type
>
>   File "/home/t-iris2-011/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
> line 1916, in open
>     raise ValueError, "Unknown model type"
>
> See reply log for Python traceback.
>
> does it the problems with the python variables? In my *.bashrc file I
> have sourced the pathways to both chimeras in the following manner:
>
> export PATH=$PATH:/home/t-iris2-011/.local/UCSF-Chimera64-1.12/bin:/home/t-iris2-011/.local/UCSF-Chimera64-batch/bin
>
>
>
>
> James
>
> 2017-12-05 20:32 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:
>> Just try the Chimera findclash command and figure out what options you want.  When you have one command that works the way you want, you can use bash to make a plain text file containing many such commands (Chimera command script file, *.com).  The command would be something like
>>
>> findclash :.b test other
>>
>> … but you would have to give additional options with the values you want to use (overlapCutoff, hbondAllowance etc.).  See the documentation:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
>>
>> We can’t do the exact script for you because everybody’s situation is slightly different.  You have actually try entering some commands.
>> Elaine
>>
>>
>>> On Dec 5, 2017, at 1:24 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>
>>> Thank you so much for the suggestions, Elaine!
>>>
>>> In fact I have assigned chains (I guess as chain IDs) using Chimera's
>>> GUI interface, which I have mentioned in the another topic.
>>> For the simplicity I would use Chimera's scripting interface for the
>>> batch mode (will be grateful for the example of the script because I
>>> am also very bad in the programming!) e.g to check the contacts
>>> between chain A and "all other atoms" in only one pdb  file (not a
>>> trajectory).
>>>
>>> BTW, via bash I can produce several such scripts (for each of the
>>> chains) and execute them in a loop manner, doesn't it?
>>> e.g to check contacts between chain B and "all other atoms".
>>>                                   between chain C and "all other atoms" etc ..
>>>
>>>
>>> James
>>>
>>> 2017-12-04 18:57 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu>:
>>>> Hi James,
>>>> I don’t know how you have assigned these letters (as aliases? chain IDs? residue names?) but first figure out the “findclash” command that does the same thing you were doing with the Find Clashes/Contacts GUI.
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>>>>
>>>> There are two main kinds of Chimera scripts, Chimera commands and Python.  Python can have Chimera commands embedded, and is generally needed if you want to substitute arguments into the commands or loop through many variations of the command or a large set of PDB files.  Python is also needed for actions for which no Chimera command is available.
>>>>
>>>> I’m not a programmer myself so I can only point to information others have generated… there’s always the programmer’s guide:
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>
>>>>
>>>> In this case after figuring out the findclash command options you want, I guess you could write a python script to substitute in the letters into the command to loop through the monomers.  There is a page on how to loop through multiple different structures, which is different, but may still be helpful:
>>>> <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>>>>
>>>> There are lot of example Chimera python scripts for miscellaneous tasks here:
>>>> <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
>>>>
>>>> After you figured out a script for an individual PDB, you could adapt it to specify a per-frame script in MD Movie for your trajectory.
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
>>>>
>>>> I hope this helps,
>>>> Elaine
>>>> ----------
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>>
>>>>> On Dec 4, 2017, at 5:37 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>>>
>>>>> One question regarding Find Clashes/Contacts.
>>>>>
>>>>> assuming that I have assigned the unique letters for each of the monomer
>>>>> in my CG system. Now I am using this selection ("the individual
>>>>> chain" vs "all other systems") to calculate contacts using -2.2 cutoff
>>>>> for MARTINI (operating with the backbone atoms only). Is it possible
>>>>> to run the same routine in batch mode i) for the individual pdb as
>>>>> input as well as ii) for the md trajectory (to calculate occurence of
>>>>> the contacts along the trajectory)? I would be very grateful for some
>>>>> example script file for batch Chimera!
>>>>>
>>>>> James
>>>>
>>>
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>>