[Chimera-users] Recursive structure matching and acquisition of descriptive numbers

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 20 11:30:38 PDT 2016


Hi Joe,
	I guess the first thing is that the command equivalent for MatchMaker is “matchmaker” or “mmaker”, not “match”.  The “match” command is for when you know a priori the exact set of atoms you want matched in the two structures.  “matchmaker” is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure.  The documentation for the matchmaker command is here:

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options>

I looked at your script and didn’t see anything obviously wrong.  What exactly isn’t working?  And unfortunately the answer is no, you can’t run a GUI  operation and easily find the command equivalent.  ChimeraX will have that capability though.

—Eric


> On Sep 20, 2016, at 5:07 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> 
> Hi again,
> 
> I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information.
> 
> Is there are resource with more information on the commandline implementation of match anywhere other than the link below?
> 
> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options>
> 
> I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html>
> 
> But I can't quite unwrap the options specified in the command for my uses.
> 
> Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed?
> 
> I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 <http://pastebin.com/6k9cew55> incase it gives you some indication of what I'm attempting to do.
> 
> Many thanks
> 
> 
> Joe Healey
> 
>                                        
> M.Sc. B.Sc. (Hons)
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
> 
> Jointly working in:
> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
> 
> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
> From: Greg Couch <gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>>
> Sent: 08 September 2016 22:43:55
> To: Healey, Joe; chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB
> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
>  
> chimera --nogui can't access graphics.  Headless chimera has software OpenGL rendering, so it can be used to create images.  Make sure to use the windowsize command to set the size of the framebuffer.  Don't know if pychimera cares.
> 
>     -- Greg
> 
> On 09/08/2016 11:53 AM, Healey, Joe wrote:
>> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin.
>> 
>> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either
>> 
>> 
>> Joe Healey
>> 
>>                                        
>> M.Sc. B.Sc. (Hons)
>> PhD Student
>> MOAC CDT, Senate House
>> University of Warwick
>> Coventry
>> CV47AL
>> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
>> 
>> Jointly working in:
>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
>> 
>> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
>> From: Greg Couch <gregc at cgl.ucsf.edu> <mailto:gregc at cgl.ucsf.edu>
>> Sent: 07 September 2016 19:49:19
>> To: Healey, Joe; chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB
>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
>>  
>> Yes, Chimera's Python code is only "warrantied" to work with its own Python.  See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b>, for how to install other software into Chimera.  Other parts of the FAQ may help you too.
>> 
>> That said, Jaime Rodríguez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html>, and came up with pychimera, https://pypi.python.org/pypi/pychimera <https://pypi.python.org/pypi/pychimera>.  I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you.
>> 
>>     HTH,
>> 
>>     Greg
>> 
>> On 09/07/2016 07:36 AM, Healey, Joe wrote:
>>> Hi Eric,
>>> 
>>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however.
>>> 
>>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in?
>>> 
>>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!).
>>> 
>>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'.
>>> 
>>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script.
>>> 
>>> Do you have any advice about how best to proceed?
>>> 
>>> Many thanks,
>>> 
>>> Joe Healey
>>> 
>>>                                        
>>> M.Sc. B.Sc. (Hons)
>>> PhD Student
>>> MOAC CDT, Senate House
>>> University of Warwick
>>> Coventry
>>> CV47AL
>>> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
>>> 
>>> Jointly working in:
>>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
>>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
>>> 
>>> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
>>> 
>>> From: Eric Pettersen <pett at cgl.ucsf.edu> <mailto:pett at cgl.ucsf.edu>
>>> Sent: 31 August 2016 18:23
>>> To: Healey, Joe
>>> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
>>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
>>>  
>>> Hi Joe,
>>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically.  The mailing list gives the attachment a “.bin” extension but it’s really a .py file.  Just change the extension if you need to.  Let me know if you have any questions about how to adapt the script to your needs…
>>> 
>>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html>
>>> 
>>> —Eric
>>> 
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>> 
>>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins.
>>>> 
>>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm.
>>>> 
>>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log?
>>>> 
>>>> Thanks
>>>> 
>>>> Joe Healey
>>>> 
>>>>                                        
>>>> M.Sc. B.Sc. (Hons)
>>>> PhD Student
>>>> MOAC CDT, Senate House
>>>> University of Warwick
>>>> Coventry
>>>> CV47AL
>>>> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
>>>> 
>>>> Jointly working in:
>>>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
>>>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
>>>> 
>>>> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>_______________________________________________
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>>> 
>>> 
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>> 
> 
> 

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