That sounds very promising, I'll rework the script for pychimera and see how I get on.
Many thanks for all the help.
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@warwick.ac.uk
Jointly working in:
Waterfield Labhttp://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldl... (WMS Microbiology and Infection Unit)
and the Gibson Labhttp://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/ (Warwick Chemistry)
Twitter: @JRJHealeyhttps://twitter.com/JRJHealey | Website: MOAC Pagehttp://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey
________________________________
From: Greg Couch
Sent: 07 September 2016 19:49:19
To: Healey, Joe; chimera-users@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, 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, and came up with 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@warwick.ac.ukmailto:J.R.J.Healey@warwick.ac.uk
Jointly working in:
Waterfield Labhttp://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldl... (WMS Microbiology and Infection Unit)
and the Gibson Labhttp://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/ (Warwick Chemistry)
Twitter: @JRJHealeyhttps://twitter.com/JRJHealey | Website: MOAC Pagehttp://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey
________________________________
From: Eric Pettersen mailto:pett@cgl.ucsf.edu
Sent: 31 August 2016 18:23
To: Healey, Joe
Cc: chimera-users@cgl.ucsf.edumailto:chimera-users@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
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
On Aug 31, 2016, at 3:02 AM, Healey, Joe mailto:J.R.J.Healey@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@warwick.ac.ukmailto:J.R.J.Healey@warwick.ac.uk
Jointly working in:
Waterfield Labhttp://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldl... (WMS Microbiology and Infection Unit)
and the Gibson Labhttp://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/ (Warwick Chemistry)
Twitter: @JRJHealeyhttps://twitter.com/JRJHealey | Website: MOAC Pagehttp://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey
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