[Chimera-users] command line clustering (how to select a subSection?)
Eric Pettersen
pett at cgl.ucsf.edu
Fri Jun 4 11:48:10 PDT 2021
Hi Laura,
When Conrad wrote this code he must not have tested this alternate code path, but it almost works. You just need to add "from chimera import selection" right above the "s = selection.OSLSelection(osl)" line (line 100). When I add that, the script works for me.
--Eric
> On Jun 4, 2021, at 11:22 AM, Laura Morris via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Eric,
>
> First of all, thanks for your help so far. If you can take a look at the next problem, I would appreciate it.
>
> I think the string suggestion worked for what I asked, but it appears there's another issue with the script. I realize I'm using code that's > 10 yrs old (and things change) but if you (or someone) know what's not right about this next section this would help me not have to recode NMRCLUST from scratch (which is tempting, but not preferable). OR, if someone knows where NMRCLUST might be available, I'd be happy to download it.
>
> If I don't change anything in the original script, it runs fine (using all heavy atoms presumably). When I change the value of subSelection (given Eric's example string), it runs through the RMSD portion (I think, I get 250 groups of "Running ksdssp" comments, like below). Then it appears to get hung up in the function _getAtoms
>
> I am running basically what is referred to in the original (2010) posting, namely:
> chimera --nogui 3c4s.test.pdb cluster.py
>
> The 3c4s.test.pdb is 250 frames from an AMBER md run (just for testing this). The script cluster.py is the same as the one posed from 2010, with the exception of changing subSelection (to subSelection = "@CA" in this case). My Chimera version is "chimera candidate version 1.15 (build 42258) 2020-12-18 05:17:29 UTC" (in case that matters at all).
>
> [portion of code from cluster.py referred to by output of running script]
> def _getAtoms(m, subSelection):
> if not subSelection:
> #atoms = m.sortedAtoms()
> atoms = m.atoms
> else:
> osl = '%s%s' % (m.oslIdent(), subSelection)
> s = selection.OSLSelection(osl)
> wanted = s.vertices(asDict=True)
> #atoms = [ a for a in m.sortedAtoms() if a in wanted ]
> atoms = [ a for a in m.atoms if a in wanted ]
> return atoms
>
>
> [end of the output from running script]
> Computing secondary structure assignments...
> Computed secondary structure assignments (see reply log)
> Model 0.250 (3c4s.test.pdb) has no secondary structure assignments. Running ksdssp.
>
> Computing secondary structure assignments...
> Computed secondary structure assignments (see reply log)
> Compiling cluster.py...
> Compiling cluster.py succeeded
> Executing cluster.py...
> Computing distance matrix
> 0.02: created distance matrix
>
> Traceback (most recent call last):
> File "/opt/UCSF/Chimera64-1.15rc/share/chimeraInit.py", line 760, in init
> chimera.openModels.open(a, prefixableType=1)
> File "/opt/UCSF/Chimera64-1.15rc/share/chimera/__init__.py", line 1960, in open
> models = func(filename, *args, **kw)
> File "/opt/UCSF/Chimera64-1.15rc/share/chimera/__init__.py", line 1330, in _openPython
> loadFunc(sandboxName, fileName, f)
> File "cluster.py", line 113, in <module>
> main()
> File "cluster.py", line 12, in main
> clusterInfo = _cluster(modelList, subSelection)
> File "cluster.py", line 23, in _cluster
> for m in modelList ]
> File "cluster.py", line 100, in _getAtoms
> s = selection.OSLSelection(osl)
> NameError: global name 'selection' is not defined
>
> Error while processing cluster.py:
> NameError: global name 'selection' is not defined
>
> File "cluster.py", line 100, in _getAtoms
> s = selection.OSLSelection(osl)
>
> See reply log for Python traceback.
>
>
>
>
> Laura
>
> -----
> Laura C. Morris
> Scientific Computing Professional
> Edison & Prestegard Labs
> Complex Carbohydrate Research Center
> 706-542-6286 (lab 1075)
>
>
> From: Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
> Sent: Friday, June 4, 2021 11:36 AM
> To: Laura Morris <lcmorris at uga.edu <mailto:lcmorris at uga.edu>>
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: Re: [Chimera-users] command line clustering (how to select a subSection?)
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
> Hi Laura,
> Looking at the code from that mail, the subSelection is just a string with the atom spec you want, but without the model number part. So for carbon alphas it would be "@CA". For the example you gave it would be ":3-55 at CA".
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Jun 4, 2021, at 8:07 AM, Laura Morris via Chimera-users <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
>>
>> Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html>) that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code:
>>
>>
>> def main():
>> import chimera
>> modelList = chimera.openModels.list(modelTypes=[chimera.Molecule])
>> subSelection = None # Change this to CAs or heavy atoms
>> clusterInfo = _cluster(modelList, subSelection)
>> saveReps(clusterInfo, "reps.pdb") # Change file name if needed
>>
>> The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55 at CA". I know there's a "runCommand" function that can be included (using "from chimera import runCommand"). Is this used in some way to set subSelection, and if so, how?
>>
>> Any help is appreciated.
>>
>> Regards,
>>
>> Laura
>>
>> -----
>> Laura C. Morris
>> Scientific Computing Professional
>> Edison & Prestegard Labs
>> Complex Carbohydrate Research Center
>> 706-542-6286 (lab 1075)
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210604/6cf9bfb6/attachment.html>
More information about the Chimera-users
mailing list