Re: [PyMOL] list of polar contacts

2012-02-03 Thread Abhinav Verma
Great!! Thanks to all !!.. and specially Takanori!! Cheers, Abhi On Wed, Feb 1, 2012 at 6:09 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Thomas, > > > alternate locations and multi-state objects should not be an issue, the > > script on the PyMOLWiki can handle both! The o

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Jason Vertrees
Hi Thomas, > alternate locations and multi-state objects should not be an issue, the > script on the PyMOLWiki can handle both! The only issue would be altering > coordinates after distance objects have been created (and having > dynamic_measures = off). I just read over your change to Takanori's

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Thomas Holder
Jason, alternate locations and multi-state objects should not be an issue, the script on the PyMOLWiki can handle both! The only issue would be altering coordinates after distance objects have been created (and having dynamic_measures = off). Nevertheless, I'm glad you plan to provide a real C

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Jason Vertrees
Thomas, When you hash by coordinates you could get odd results from alternate locations and multi-state objects. I like how Takanori solved the problem, but it's not a strictly perfect solution. What I need to do is provide access to the C-object for real. We plan to provide something for this soo

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Thomas Holder
Jason, what pitfalls? Are they still present in this script? http://pymolwiki.org/index.php/Get_raw_distances Cheers, Thomas On 02/01/2012 04:01 PM, Jason Vertrees wrote: > Takanori, > > This is a very clever script -- well done! There are some pitfalls, > but in general this should work well

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Takanori Nakane
Dear Thomas, > Takanori, Looks like you've studied the output of cmd.get_session quite > well. Would you mind to share some of your insights by putting > documentation on http://pymolwiki.org/index.php/Get_session ? I have a plan to write some documentation of Pymol's internal data structure an

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Jason Vertrees
Takanori, This is a very clever script -- well done! There are some pitfalls, but in general this should work well. Cheers, -- Jason On Tue, Jan 31, 2012 at 6:01 PM, Takanori Nakane wrote: > Hi Abhinav and Jason, > >> The underlying C-object for a measurement does not support >> iterate/alter.

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Thomas Holder
On 02/01/2012 12:01 AM, Takanori Nakane wrote: > Hi Abhinav and Jason, > >> The underlying C-object for a measurement does not support >> iterate/alter. This is rather silly; PyMOL should be able to tell you >> what's in the object. > > As an ad-hoc hack, I wrote a Python script to access internal

Re: [PyMOL] list of polar contacts

2012-02-01 Thread Thomas Holder
On 01/31/2012 05:03 PM, Jason Vertrees wrote: > Please file a feature request on the open-source bug tracker and we'll > be sure to look at this ASAP. no need for a duplicate, it's already there: http://sourceforge.net/tracker/?func=detail&aid=3326957&group_id=4546&atid=354546 Cheers, Thomas

Re: [PyMOL] list of polar contacts

2012-01-31 Thread Takanori Nakane
Hi Abhinav and Jason, > The underlying C-object for a measurement does not support > iterate/alter. This is rather silly; PyMOL should be able to tell you > what's in the object. As an ad-hoc hack, I wrote a Python script to access internal C-object of distance representation and convert it to at

Re: [PyMOL] list of polar contacts

2012-01-31 Thread Jason Vertrees
Hi Abhinav, The underlying C-object for a measurement does not support iterate/alter. This is rather silly; PyMOL should be able to tell you what's in the object. Please file a feature request on the open-source bug tracker and we'll be sure to look at this ASAP. Cheers, -- Jason On Tue, Jan

Re: [PyMOL] list of polar contacts

2012-01-31 Thread Abhinav Verma
Hi thanks, still it is not the same.. But thanks.. I wish Jason can reply if there is any way to get the list from the apply command. thanks, Abhi On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis wrote: > I think you can reproduce the results from "apply->find->polar contacts" > option wit

Re: [PyMOL] list of polar contacts

2012-01-30 Thread Thomas Evangelidis
I think you can reproduce the results from "apply->find->polar contacts" option with the PyMOL built-in "distance" command. E.g. distance hbonds, all, all, 3.2, mode=2 The problem is that you cannot set the A-H-D angle which is important for the definition of the H-bond. On 30 January 2012 18:4

Re: [PyMOL] list of polar contacts

2012-01-30 Thread Thomas Evangelidis
Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use list_hbonds.py from: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ and set the cutoff and angle to the values you wish. Thomas On 30 January 2012 16:34, Abhinav Verma wrote: > Hi

[PyMOL] list of polar contacts

2012-01-30 Thread Abhinav Verma
Hi, I am trying to get the list of hbonds formed using Apply-find-polarcontacts. I searched and found some scripts, but they never give me the same result as the one by default pymol. Any ideas how I can get the hbonds as a list. Thanks, Abhinav -