VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 11 2015 - 18:03:49 CDT

On Sat, Apr 11, 2015 at 5:57 PM, surya narayanan chandrasekaran
<sonofsunsurya_at_gmail.com> wrote:
> Hi,
>
> Is there a command exist to get list of non standard residues. I have more
> than thousands of non-standard residues in my protein and they are different
> by five types. I need seg id and residue id of them. I know the question so
> general. but a idea would be great

build a selection that contains a common atom type (say CA for the
alpha carbon) and then the desired residue names, either with a
regular expression or through logical or). from this selection
function you can now get multiple properties in one go, e.g. resid,
resname, segid and in return you will get a list of lists that
contains the requested property triple for each matched atom in the
selection (and since there usually is only one alpha carbon per
residue, that will be identical to one triple per residue).

that list you can either output to a file, or process further with
additional tcl scripting.

axel.

>
> --
> Surya
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.