VMD-L Mailing List

From: Ioana Cozmuta (icozmuta_at_mail.arc.nasa.gov)
Date: Tue Mar 14 2006 - 18:17:46 CST

Hi John,

This is what I want to select from my entire structure:
the DNA strand
the protein aminoacids 2A away from certain numbered residues
the common water molecules within 2 of protein and DNA

I came up with the following that I just cant use in a script. I want
the selection below to be written out from several frames of a
trajectory. That's why I want to define the selection only once and then
use the $sel writexyz test.xyz command to write it out.

((nucleic or resname RA5 or resname RA3) or (protein and same residue as within 2 of (protein and resid 11 23 35 47 59 71 83)) or ((resname SPM and same residue as within 2 of (nucleic or resname RA5 or resname RA3)) and (resname SPM and same residue as within 3 of (protein and same residue as within 2 of (protein and resid 11 23 35 47 59 71 83)))))

Any help would be greatly appreciated.
Thanks,
Ioana

John Stone wrote:
> Ioana,
> Have you tried using atom selection macros to help make your selection
> text a little more compact?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Mar 14, 2006 at 04:00:27PM -0800, Ioana Cozmuta wrote:
>
>> Hi,
>>
>> I have a very long selection that I want to define however it seems that
>> I reach the max number of characters allocated by default for a
>> selection. I could split the selection in smaller parts but I don't know
>> how to write all of them after that in the same output file. Is there a
>> way to 'append' information into an output file?
>>
>>
>> Thanks,
>> ioana
>>
>> --
>> Ioana Cozmuta, Ph.D
>> Eloret Corporation
>> NASA Ames Research Center
>> Mail Stop 230-3
>> Moffett Field, CA 94035
>> phone (650) 604-0993
>> e-mail: icozmuta_at_mail.arc.nasa.gov
>> http://people.nas.nasa.gov/~ioana/
>>
>
> 

-- 
Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993
e-mail: icozmuta_at_mail.arc.nasa.gov
http://people.nas.nasa.gov/~ioana/