Yes, sorry, the frames are mapped to states. Ah, yes, that is what I
needed, that 'state' keyword argument was not listed in the wiki page.
For posterity's sake, a couple of minor modifications were required in
the code you provided.
python
for i in range(1,41):
cmd.select("wat_" + str(i),"resn WAT in <mdobjetct> within 6 of
<residue_of_interest>", state=i)
python end
I removed the byres command because I have more then 10000 water
molecules in my system and the residue ID's were rolling over and waters
far from the residue of interest were being selected.
If anyone has a suggestion on this, please let me know, I would like to
select whole water molecules for making figures.
Thanks,
Matt
On 07/01/2013 02:10 PM, Jordan Willis wrote:
> I know you have asked for frames, but I assume that each frame is mapped to a
> state. The selection logic allows for you to specify the state.
>
> So if the waters of interest are in state 1,40:
>
> python
> for i in range(1,41):
> cmd.select("wat_"+i,"byres in <mdobjetct> within 6 of
> <residue_of_interest>",state=i)
> python end
>
> J
>
>
>> 'sele wats, byres res
>> WAT in <md_obj> within 6 of
>> <residue of interest>',
>
>
> On Jul 1, 2013, at 12:42 PM, Matthew Baumgartner <mp...@pitt.edu> wrote:
>
>> Hi,
>> Is it possible to force a selection to only apply to the specific frame
>> rather then across frames?
>> I'm running in to a problem where I have some (~40) frames from an
>> explicit solvent MD that I want to look at. What I want to do is look at
>> water molecules around a specific residue at each frame, but when I do
>> something like, 'sele wats, byres resn WAT in <md_obj> within 6 of
>> <residue of interest>', it ends up a majority of the waters in the
>> system. I think that what it is doing is finding all waters that are
>> with 6 A of the residue of interest in ALL frames, then selecting them
>> in the current frame. Which is not the expected behavior.
>>
>> From what I can tell, there isn't a selection syntax for selecting the
>> frame. Perhaps there is a setting for this that I couldn't find.
>>
>> Any help would be appreciated including solutions involving VMD or
>> custom scripts.
>>
>> Thanks,
>> Matt
>>
>> --
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
