[PyMOL] list of atomic coordinates involved in solvent accessible area

 Hi pymol  community,  How I can get the atomic list and coordinates involve in solvent accessible area from PDB structure using pymol. Any suggestion regarding program or script would be great.  thank you Regards,Sajid--

[PyMOL] List

Could you please take my email off the PyMOL user list. Thanks, Everly FLEISCHER Sent from my iPad -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce vers

Re: [PyMOL] List residues functionality ?

Hi Carsten & Jason, this is what I would do: @cmd.extend def list_resi(selection='all'): resi_list = [] cmd.iterate('byca (%s)' % selection, 'resi_list.append(resi);' 'print "/%s/%s/%s/%s`%s" % (model, segi, chain, resn, resi)', space=locals()) return resi_list

Re: [PyMOL] List residues functionality ?

Carsten, What about http://www.pymolwiki.org/index.php/List_Selection and http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar script for retrieving object names: http://www.pymolwiki.org/index.php/GetNamesInSel. Cheers, -- Jason On Fri, Jan 31, 2014 at 10:30 AM, Schubert,

[PyMOL] List residues functionality ?

Hi All, probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not flexi

Re: [PyMOL] list of polar contacts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 -

Re: [PyMOL] list of hydrogen bonds

Hi Martin, On Wed, 11 Aug 2010 12:02:32 +0200 Martin Hediger wrote: > I was thinking about this as well, I saw an older post on this topic > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html > but it seems that the script mentioned there starts to see 'hydrogen > bonds

Re: [PyMOL] list of hydrogen bonds

I was thinking about this as well, I saw an older post on this topic http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html but it seems that the script mentioned there starts to see 'hydrogen bonds' between non-polar hydrogens and atoms up to 15 angstrom away. Can someone con

Re: [PyMOL] list of hydrogen bonds

Hi Jason, is it possible to print out a list of hydrogen bonds found by polar contacts. Maia -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: htt

Re: [PyMOL] List of Groups

David, I think groups are treated like objects (see "help group"). So, one can type print cmd.get_names("objects") and all the objects (proteins, groups, etc) will be returned. For example: group a group b group c print cmd.get_names("objects") The problem is that other objects will

[PyMOL] List of Groups

How would someone get the list of groups in a pymol session? get_object_list doesn't have them and the only commands I can find in cmd that have the word "group" in them seems to be group and ungroup (if my quick regex search worked right). Thanks, David

Re: [PyMOL] list residues in a selection

Hi, * Michael George Lerner [2005-07-06 09:28] wrote: > > On Wed, 6 Jul 2005, Sebastien Gerega wrote: > > >Is there a way to list the residues that are in a selection? For example > >if I use the command "select near, sel01 around 6" how can I obtain a list > >of the residues in the "near" s

Re: [PyMOL] list residues in a selection

I asked a similar question a while ago, and Kristan Rother archived the answer at . Here it is: Using PyMOL commands: list=[] iterate (name ca),list.append((resi,resn)) print list [('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HI

Re: [PyMOL] list residues in a selection

On Wednesday 06 July 2005 08:58, Sebastien Gerega wrote: > Is there a way to list the residues that are in a selection? For example > if I use the command "select near, sel01 around 6" how can I obtain a > list of the residues in the "near" selection? Using cmd.get_pdbstr("near") (after "import

[PyMOL] list residues in a selection

Is there a way to list the residues that are in a selection? For example if I use the command "select near, sel01 around 6" how can I obtain a list of the residues in the "near" selection? thanks, Sebastien

Re: [PyMOL] List participation commentary......

On Wed, 17 Nov 2004 10:48:49 -0800 (PST), Thomas Stout wrote: Hi All -- Recently I've noticed a growing number of questions being posed to the PyMOL mailing list that never seem to get responses. I infer from this that one or both of two things are happening: either 1) list members that kn

[PyMOL] List participation commentary......

Hi All -- Recently I've noticed a growing number of questions being posed to the PyMOL mailing list that never seem to get responses. I infer from this that one or both of two things are happening: either 1) list members that know the answers to these questions are not responding to the questions