Re: [PyMOL] polar contacts involving F, Cl and S atoms

[Thomas E. <te...@mb...>]

I see what the abbreviations mean now, so stands for small overlap, bo  
for bad overlap, wc Van Der Wals contact, etc. They are at the left  
side of King's GUI. Sorry that was a naive question.

Tom

> Tom,
>
> The simplest thing to do is just to use the dist command to check the
> interactions manually.
>
> dist atom1, atom2
>
> If you have a bunch to look at and the ligands are in the PDB then
> MolProbity can do contact analysis so you can pull out Hydrogen bonds
> that way.
>
> If no one has a better guess, maybe try 1.7 plus the VDW radii of F
> (1.35), Cl (1.8), or S (1.85).  Seems like a good guess to me.
>
> Cheers,
> -bob
>
> On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis  
> <te...@mb...> wrote:
>> Hi Pymol users,
>>
>> I want to display the polar interactions between some ligands and a
>> receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S
>> atoms. There's a tutorial on the wiki that explains how to set the
>> cutoff distance but that refers only to O and N atoms:
>>
>> http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
>>
>>  I was wondering if I can do that by modifying those code snippets. I
>> would greatly appreciate any help. Also if someone knows the distance
>> H-bond donor and acceptor for F and Cl atoms please tell me. I know
>> only  the respective distance for S which is 4 A maximum.
>>
>> thanks,
>> Tom
>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>


----- End message from imm...@gm... -----