VMD-L Mailing List

From: Jacob Durrant (jacobdurrant_at_gmail.com)
Date: Tue Feb 25 2014 - 23:49:38 CST

Thanks for your help with this, Josh! I really appreciate it. I'll take a
look at the suggestions you provided. Best regards. ~Jacob

On Tue, Feb 25, 2014 at 8:44 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Jacob,
> Argh. Well, I guess a single atomselection isn't the way to go. Having
> made enough of a fool of myself, this is code I've actually tested. It'll
> work, but its a tkcon solution, not an atomselection one (so you can't
> directly visualize it).
>
> set lists [measure contacts 0.5 [atomselect top "noh"]]
> foreach i [lindex $lists 0] j [lindex $lists 1] {
> puts "Atom $i clashes with atom $j"
> }
>
> Alternatively, this will give you all the ids that are part of clashes
> (which you can then visualize with "index")
> lsort -unique -increasing -integer [join [measure contacts 0.5 [atomselect
> top "noh"]]]
>
> The real solution would be to hack together something very similar to
> within ("cwithin" or "contactwithin") that takes advantage of gridsearch so
> it doesn't need to calculate O(n^2) distances to detect clashes. It may
> already exist within the atomselection language, but I'm unaware of it. :(
>
> Hope this is more useful than my tautologically empty selections. :D
> -Josh
>
>
> On 02/25/2014 08:56 PM, Jacob Durrant wrote:
>
> Thanks for your help with this, Josh. Unfortunately, that selection didn't
> identify the steric clashes either. The selection was again empty. If I'm
> not mistaken, these are all equivalent:
>
> noh and within 0.5 of noh and not within 0.00000000001 of noh
> noh and (within 0.5 of noh) and (not within 0.00000000001 of noh)
> noh and noh and (not within 0.00000000001 of noh)
> noh and noh and (not noh)
> noh and not noh
>
> Which is why the selection was empty.
>
> I'd really appreciate any other ideas. Detecting steric clashes is a
> pretty common task. It would be wonderful if I didn't have to write my own
> code to detect them, especially since VMD's selection code is so fast, even
> on large systems.
>
> Thanks,
>
> Jacob
>
>
>
>
> On Tue, Feb 25, 2014 at 7:28 PM, Josh Vermaas <vermaas2_at_illinois.edu>wrote:
>
>> Hi Jacob,
>>
>> Ahh... Right. I use exwithin on single residues, so in that case it works
>> as I explained, however the exwithin line I gave you is logically
>> equivalent to "noh and within 0.5 of noh and not noh", which will always
>> yield an empty selection. :( How about "noh and within 0.5 of noh and not
>> within 0.00000000001 of noh"? This detects steric clashes where the atoms
>> are not literally on top of one another. This is probably good enough for
>> most instances, so long as you remember that if psfgen can't guess a
>> position, it puts the atom at the origin, and so you should also make sure
>> the number of atoms at the origin isn't greater than 1.
>>
>> -Josh
>>
>>
>> On 02/25/2014 12:28 AM, Jacob Durrant wrote:
>>
>> Hi all. Thanks for your help with this. I'm still having some troubles.
>> To test these selections, I downloaded a PDB and intentionally moved the
>> atom of one residue so it's very close to an atom of another (a steric
>> clash).
>>
>> The selection ((noh within 0.5 of noh) and not same residue as
>> 'residue') gave an error (atom selection could not be understood). Same
>> with ((noh within 0.5 of noh) and not same residue as residue).
>>
>> The selection (noh and exwithin 0.5 of noh) didn't give an error, but
>> it didn't select anything, not even the two atoms that were only 0.25 Å
>> apart.
>>
>> In case it's helpful, I'm attaching the PDB with the steric clash for
>> testing. Thanks for your help!
>>
>> ~Jacob
>>
>>
>> On Sat, Feb 22, 2014 at 4:49 PM, Josh Vermaas <vermaas2_at_illinois.edu>wrote:
>>
>>> You are very close. noh and exwithin 0.5 of noh. "exwithin" is
>>> basically the "within" keyword, but an atom is excluded from its own within
>>> list.
>>> -Josh Vermaas
>>>
>>>
>>> On 02/21/2014 09:56 PM, Jacob Durrant wrote:
>>>
>>> Hi all. Is there an atom selection to identify steric clashes? At first
>>> I thought something like "noh within 0.5 of noh" might work, but each atom
>>> is identified as being very near itself, so this section ends up being
>>> equivalent to "all".
>>>
>>> Thanks,
>>>
>>> Jacob
>>>
>>> --
>>> ==============================
>>> Jacob D. Durrant <https://amarolab.ucsd.edu/%7Ejdurrant/>, PhD
>>> Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
>>> University of California, San Diego
>>>
>>> Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
>>> jacobdurrant_at_gmail.com
>>> jdurrant_at_ucsd.edu
>>>
>>>
>>>
>>
>>
>> --
>> ==============================
>> Jacob D. Durrant <https://amarolab.ucsd.edu/%7Ejdurrant/>, PhD
>> Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
>> University of California, San Diego
>>
>> Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
>> jacobdurrant_at_gmail.com
>> jdurrant_at_ucsd.edu
>>
>>
>>
>
>
> --
> ==============================
> Jacob D. Durrant <https://amarolab.ucsd.edu/%7Ejdurrant/>, PhD
> Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
> University of California, San Diego
>
> Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
> jacobdurrant_at_gmail.com
> jdurrant_at_ucsd.edu
>
>
> 

-- 
==============================
Jacob D. Durrant <https://amarolab.ucsd.edu/~jdurrant/>, PhD
Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
University of California, San Diego
Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
jacobdurrant_at_gmail.com
jdurrant_at_ucsd.edu