From: Dennis N Bromley (dbromley_at_uw.edu)
Date: Sat Jun 04 2011 - 13:09:48 CDT

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-
>>>
>>>
>>>
>>>
>>>
>>
>>
>