Hi Hernando, Here’s some Python that gets the residues of a molecule. There is no Python chain object but the code shows how to get the chain ids. Also it shows atom.xformCoord() that gets the transformed coordinate. The transformed coordinate includes any rotation and translation you did with the mouse. Tom import chimera sel = chimera.selection.OSLSelection('#0') sel.models() -> [<_molecule.Molecule object at 0x11696ac10>] m = sel.models[0] r = m.residues len(r) -> 76 type(r) -> <type 'list'> r0 = r[0] r0.id.chainId -> u'A' set(r0.id.chainId for r0 in r) -> set([u'A', u'B']) a = r0.atoms[0] a.xformCoord() -> chimera.Point(15.491, 7.05, 17.165)
On Oct 25, 2018, at 1:35 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
An additional question: Is it possible to retrieve the atomic coordinates after a transformation (e.g. after an align/superposition operation) rather than the original coordinate values?
e.g. I am currently using the following commands to retrieve the coordinates (x,y,z) of the CA atom in model,residue,chain atom = chimera.selection.OSLSelection("#%d:%d.%c@CA" % (model,residue,chain)).vertices() (x,y,z) = atom[0].coord()
However, this retrieves the original coordinates not the coordinates after a transformation.
Thanks
Hernando
Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>
From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Hernando J Sosa Sent: Thursday, October 25, 2018 12:50 PM To: chimera-users BB Subject: [Chimera-users] python script
Dear Chimera,
I am writing a Chimera python script and need to get a list of the chains and residue numbers of specific opened models . What would be the command/syntax to do that? or can you point me to a code example where something like this is done.
Thanks
Hernando
From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>] On Behalf Of Hernando J Sosa Sent: Monday, June 11, 2018 2:46 PM To: Eric Pettersen Cc: chimera-users BB Subject: Re: [Chimera-users] python script
Thanks Eric,
These alternatives is what I was looking for.
Best
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>] Sent: Friday, June 08, 2018 7:27 PM To: Hernando J Sosa Cc: chimera-users BB Subject: Re: [Chimera-users] python script
Hi Hernando, Perhaps runCommand should return a value but it doesn’t. The reasoning there was that the argument to runCommand could be anything, including several commands separated by semi-colons, so in some cases it’s confusing what the return value should be. In any case that ship has sailed and you have to do something else to get the value. In most cases it calling the underlying function that performs the command and using it’s return value, but looking at the code that implements the “measure center” command I can see that it doesn’t return anything either. So in the particular case of the example you provided, I can see two options for getting the value:
Option 1) atoms = chimera.selection.OSLSelection(“#0:.A@CA”).vertices() center = chimera.Point([a.coord() for a in atoms]) x, y, z = center.data()
Option 2) rc(“sel #0:.A@CA”) center = chimera.Point([a.coord() for a in chimera.selection.currentAtoms()]) x, y, z = center.data()
I hope this helps.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 8, 2018, at 11:10 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Dear Chimera,
Is it possible to assign the result of running a chimera command in python to a string or something else? E.g doing something like:
from chimera import runCommand as rc myresult = rc('measure center #0:.A@CA')
And then using the myresults somewhere else in the script after parsing for the relevant values?
Maybe there is a n easier way to accomplish this?
Thanks
Hernando
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