[chimera-dev] Non-standard residues

[Alex Gawronski]

Hello,

I used :/!isHet for the "spec" option for "minimize" and I'm still getting
"Unable to find GAFF type for #0:155.A at FE " for 101M. I thought this would
skip the heme, but I guess not. How can I avoid this error?

Thanks again!

Alex

On Tue, Jul 14, 2009 at 5:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20090714/9994afac/attachment.html>