On Sep 22, 2017, at 2:52 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi again Chimera Team,
I have a large macromolecular structure, and I want to, at random, substitute some of the separate models for a variant form.
Is it possible to do this through chimera, e.g. via python? It seems to me it would basically be a case of:
enumerate the list of open models
chimera.openModels.list() returns a list of all open models (including volume models, etc.); to get a list of just the molecular models: from chimera import openModels, Molecule mols = openModels.list(modelTypes=[Molecule])
pick a model at random
The Python random <https://docs.python.org/2/library/random.html#module-random> module is used for choosing things at random.
either open a new model, fit it to that model, then close the old one, or somehow get the old models co-ords, close it, then open the new one in its place from a specified file path
Off the top of my head it seems easiest to open the new model, use MatchMaker to match it on the old one, and then close the old one. So, suppose you had your random old model in a variable named old_model, then you would use code something this to replace it: from chimera import openModels, runCommand opened_models = openModels.open(“path-to-model-file”) new_model = opened_models[0] runCommand(“matchmaker #%d #%d” % (old_model.id, new_model.id)) runCommand(“close %d” % old_model.id) —Eric Eric Pettersen UCSF Computer Graphics Lab
Any alternative suggestions if there's a better way to do this would be great as well.
Thanks
Joe Healey
M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk <mailto:J.R.J.Healey@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> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>