[Chimera-users] selection (from distance) among PDB files after docking

[Damien Larivière]

Hi Elaine,

I found the problem: I put rc("close session") one line before and it 
worked:

from chimera import runCommand as rc
#from chimera.tkgui import saveReplyLog
for i in range(1, 3):
     rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex 
run_240111\Docking_results\240111\dock%04d.pdb" % i)
     rc("distance :93.B at N :131.C at N")
     rc("distance :246.B at N :131.C at N")
     rc("distance :162.B at N :135.C at N")
     rc("close session")
     #rc("saveReplyLog('replyLog%04d.txt')" % i)

Many thanks for all your suggestions!

Damien

Le 24/01/2011 20:16, Damien Larivière a écrit :
> Dear Elaine,
>
> Many thanks for your reply.
>
> I choose not to use the findclash command simply because the distance 
> between one atom of the residue (here N) and the same atom in the 
> other residue is enough for me. But I will remind the proposition.
>
> So I followed your proposition of a script and I wrote the following 
> for which I meet a chimera error:
>
> from chimera import runCommand as rc
> #from chimera.tkgui import saveReplyLog
> for i in range(1, 3):
>     rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex 
> run_240111\Docking_results\240111\dock%04d.pdb" % i)
>     rc("distance :93.B at N :131.C at N")
>     rc("distance :246.B at N :131.C at N")
>     rc("distance :162.B at N :135.C at N")
>     #rc("saveReplyLog('replyLog%04d.txt')" % i)
> rc("close session")
>
> It says that Chimera has to open a file called dock0001.pdb, calculate 
> three distances which are sent into the replylog, close the file; then 
> open dock0002.pdb calculate three distances...
>
> I only specified "i in range (1, 3)" to test the script with just 2 
> files. When "i in range (1, 2)" Chimera effectively opens dock0001.pdb 
> and does all the distance measurements. But when "i in range (1, 3)" I 
> have an error (see the chimeraError.txt which is a copy of the ReplyLog).
>
> May you tell me what's wrong?
>
> Many thanks for your help
>
> Damien
>
>
> Le 24/01/2011 18:30, Elaine Meng a écrit :
>> Hi Damien,
>> First consider which commands you would use on each file and try them 
>> out in the command line on an example file.  If you only wanted CA-CA 
>> distances, each residue pair would require one command, something like
>>
>> dist :246.b at ca :131.c at ca
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
>>
>> That automatically sends the distance to the Reply Log.  However, it 
>> sounds like you might want to measure all pairwise distances from all 
>> atoms in one residue to all atoms in the other residue.   It could be 
>> done with a lot of distance commands naming the atoms, but one way to 
>> do it in only a single Chimera command is to stretch the function of 
>> "findclash" and force it to report all pairwise distances, something 
>> like
>>
>> findclash :83.a test :100.b overlap -100 hb 0 log true
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>>
>> The large negative overlap means to just consider everything a 
>> contact and report it even if large as 100 angstroms, hb 0 means no 
>> special treatment of H-bonds, and log true means to send all the 
>> pairwise distance information to the Reply Log.  This will be several 
>> lines of output.  To do something fancier and only output the 
>> smallest distance would require Python, which is beyond my skills.
>>
>> So let's say that for each structure, you chose to run a few 
>> "findclash" commands, one for each pair of residues.  Next consider 
>> that you will need to loop through structures.  Here is general 
>> information on how to use Python to loop through structures:
>> <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>>
>> That example also includes putting a "processing filename" message in 
>> the Reply Log.  So if you followed that general procedure, the Reply 
>> Log would have
>>
>> processing file1
>> [a bunch of lines of findclash output including distances]
>>
>> processing file2
>> [a bunch of lines of findclash output including distances]
>>
>> ... etc.
>>
>> That would still require some "manual" looking through the Reply 
>> Log.  I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Jan 23, 2011, at 10:48 AM, Damien Larivière wrote:
>>
>>> Dear all,
>>> I have numerous PDB files resulting from a docking run.
>>>
>>>  From crosslinking experiments, we know here that one way to select
>>> among all the solutions is to identify the PDB files for which the
>>> distance between some residues of interest is lower than a specific 
>>> value:
>>>
>>> distance between Res 246 in chain B and Res 131 chain C<  17 A
>>> distance between Res 162 in chain B and Res 135 chain C<  24 A
>>>
>>> The two constraints must be respected.
>>>
>>> So, is it possible to write a script which:
>>>
>>> - opens one by one the pdb files,
>>>
>>> -calculates the two distances for the current pdb file,
>>>
>>> - send in the reply log the name-number of this PDB file if it respects
>>> the two constraints?
>>>
>>> Then, I would just have a look to the reply log in order to know the 
>>> pdb
>>> files to study in depth.
>>>
>>> Many thanks for your help
>>> Damien
>>
>

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