[Chimera-users] Complete salt bridge instructions

[Simon Sham]

Thanks, Elaine! It is very helpful.

Simon________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, April 06, 2011 1:04 PM
To: UCSF Chimera Mailing List
Cc: Simon Sham
Subject: Complete salt bridge instructions

Hi Simon and others,
Here is the complete description of how to find salt bridges with findhbond.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003602.html>

I repeat the contents here, with minor revisions for clarity:

(1) Select formally charged H-bond donor and acceptor atoms,
(2) Use the FindHBond option to find only H-bonds with both ends selected. This option is in the GUI and is also available as a keyword of the findhbond command:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

Selecting charged donor/acceptor atoms:
The following command selects atom types in charged groups commonly found in amino acids and nucleotides, EXCEPT histidines:

select Ng+ | N3+ | N2+ | O2- | O3-

That's better than using residue names, because it also gets the free N-term and C-term and most charged ligand functional groups, and it is not necessary to specify "side chain only" to exclude neutral backbone hydrogen-bonding groups. However, we don't have a thiolate sulfur atom type; if there is specific Cys thiolate you wish to consider, you would have to add that sulfur to the selection manually.

Another caveat is that the selection command above does not include histidines. You could use the command:

select Ng+ | N3+ | N2+ | O2- | O3- | :his at nd1,ne2

but that would get nitrogens in neutral histidine sidechains as well as the positively charged. A more correct possibility with more steps is to: add hydrogens (AddH tool or command addh), add charge (Add Charge tool or command addcharge), and then use command:

select Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2

(The charge assignment process identifies which histidines are doubly protonated and assigns them the AMBER residue name HIP.) There are additional atom types for charged functional groups, but they would not occur in proteins. If manmade ligands are involved, however, you may want to take a look at the list of atom types and possibly add N1+,P3+,S3+,S3- (no, that's not thiolate even though it sounds like it) to the selection command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

On Apr 6, 2011, at 11:39 AM, Elaine Meng wrote:

> Hi Simon,
> The instructions you found are for the findhbond command, whereas it sounds like you are looking at the FindHBond graphical interface.
>
> You could use the findhbond command (show Command Line by choosing it from the Favorites menu), or in the FindHBond graphical interface, turn on the option to "Only find H-bonds" with setting "with both ends selected."
>
> Command instructions:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>
>
> Graphical interface instructions -- click Help button on the dialog, or view here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
>
> I guess you were looking at this earlier post,
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003577.html>
>
> I hope this helps,
> Elaine
>
>
> On Apr 6, 2011, at 11:10 AM, Simon Sham wrote:
>
>> Hi,
>> I have tried to find out salt bridges with chimera. According to the archive:
>> "findhbond selRestrict both saveFile ~/mydir/myfile"
>>
>> 1. I could not find "selRestrict" under "FindHbond".
>>
>> I am using the latest version of CHimera.
>>
>> Thanks for your help in advance.
>>
>> Best,
>> Simon Sham