[chimera-dev] Non-standard residues

[Elaine Meng]

Hi Alex,
If by standard you mean non-HETATM, then you could use Chimera command

select ~ :/isHet

or for protein and nucleic acid molecules only,

select protein | nucleic acid

If you mean "residues that are in the amber parm file and thus don't  
require running antechamber"  I don't know of a command-line specifier  
for exactly that, although the above may work in many cases.  However,  
if you use minimize with the nogui option, it can handle those  
nonstandard residues without raising a dialog, as described in the  
"minimize" page:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

For your hydrogen question, if you mean you want to allow only  
hydrogens to move, yes, that general approach will work.  Be aware  
that the command you showed, however, selects only atoms named H,  
which for proteins are just the amide hydrogens.  If you want to  
select all atoms of element H, it would be

select H

or if you want to select only polar (thus possibly H-bonding) hydrogen  
atoms, it would be

select @/idatmType=H

(type HC is hydrogens bonded to C, type H is all the other hydrogens)   
Atom type descriptions:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

I don't know what is going on with the missing object error.   
Certainly it does not occur every time DockPrep deletes atoms, and it  
probably depends on something specific in the structure you are  
working with.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Jul 13, 2009, at 5:29 PM, Alex Gawronski wrote:

> Hello,
> Is there a way to select only standard residues with the "select"  
> command?
>
> I was also wondering if this would work to minimize only H bonds:
> runCommand('select @H')
> runCommand('minimize freeze unselected nogui true')
>
> If not, how can it be done? When I try the inverse (selecting  
> everything before Hs are added), I get "ValueError: underlying C++  
> Atom object is missing", which I assume occurs because atoms are  
> removed by Dock Prep.
>
> Thanks in advance!
>
> Alex Gawronski
> Carleton University
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev