VMD-L Mailing List

From: Dennis N Bromley (dbromley_at_uw.edu)
Date: Sat Jun 04 2011 - 21:24:26 CDT

ok, another newbie question.

I can *see* all the residues now, but how do I get VMD to tell me which
residues I'm actually looking at? I'm figuring it must be some command line
thing along the lines of

resid of (my command from below)

thanks!
-denny-

On Sat, Jun 4, 2011 at 11:09 AM, Dennis N Bromley <dbromley_at_uw.edu> wrote:

> in case anyone is searching the archives later, here is an update for
> finding hydrophobic contacts.
>
> same residue as ((name "C.*") and index > 30 and within 5.4 of (index < 31
> and name "C.*") )
>
> again, however, more elegant solutions are always invited. :)
>
> -denny-
>
>
>
> On Sat, Jun 4, 2011 at 10:27 AM, Dennis N Bromley <dbromley_at_uw.edu> wrote:
>
>> not hugely elegant, but I think this will work.
>>
>> Pymol combined both structures into a single pdb for me but put my ligand
>> as atoms 1-31 and the protein atoms as 32 ->. So, no chains. However, I
>> did find that this worked:
>>
>> same residue as (within 5.4 of (index 0 to 30))
>>
>> Again, a little klugey. But it will make the figure. :)
>>
>> Any advice for a more elegant solution that doesn't involve trolling
>> through the pdb file in notepad to discover atoms numbers would be much
>> appreciated. :)
>>
>> -denny-
>>
>>
>>
>>
>>
>>
>> On Sat, Jun 4, 2011 at 10:14 AM, Dennis N Bromley <dbromley_at_uw.edu>wrote:
>>
>>> Hi Sajad,
>>>
>>> Thanks for the tip! I currently have two pdb files - actually one pdb
>>> file with the receptor and one pdbqt file from AutoDock Vina with multiple
>>> ligand poses in it. If I assume that I'm taking the best pose, I could
>>> reduce that to one and then combine the best pose with the receptor into a
>>> single PDB.
>>>
>>> Is there a simple way to handle the twp pdb file setup like I have? Or
>>> is combining them together the best way to go?
>>>
>>> thanks!
>>> -denny-
>>>
>>>
>>>
>>>
>>>
>>> On Sat, Jun 4, 2011 at 6:26 AM, sajad falsafi <sajad.falsafi_at_yahoo.com>wrote:
>>>
>>>> Hi denny,
>>>>
>>>> Please let me know that you have two PDB files or only one PDB.
>>>> if you have only one PDB file, you should type :
>>>> "chain X and same residue as within 5 of chain Y"
>>>> (istead of chain X you should type chain of receptor and istead of chain
>>>> Y type chain of ligand)
>>>> also for better analysis you can merge two of the PDB files into single
>>>> PDB.
>>>>
>>>>
>>>> hope this helps you
>>>> Sajad
>>>>
>>>> ------------------------------
>>>> *From:* Dennis N Bromley <dbromley_at_uw.edu>
>>>> *To:* vmd-l_at_ks.uiuc.edu
>>>> *Sent:* Sat, June 4, 2011 7:57:58 AM
>>>> *Subject:* vmd-l: how do I show contacts with XXX angstroms between a
>>>> protein and a ligand?
>>>>
>>>> Hi everyone,
>>>>
>>>> I'm sorry if this is a common newbie question - I've looked everywhere
>>>> including the mailing list archives. Someone did ask this question a while
>>>> ago but the response was "have you tried 'within'?" which pointed me in the
>>>> right direction but alas, I'm still having problems.
>>>>
>>>> Anyway, if someone could help me with the syntax I would be forever
>>>> grateful. I have a protein call 'receptor' and a small molecule called
>>>> 'ligand' and I'm trying to show the protein side chains that interact with
>>>> the ligand atoms. In spirit I want to write "same residue as within 5 of
>>>> (molname 'ligand)'" but I can't seem to figure out exactly how to put the
>>>> syntax together.
>>>>
>>>> Again, sorry if this has been answered somewhere and I just missed it.
>>>>
>>>> thanks!
>>>> -denny-
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>