VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Feb 24 2008 - 11:36:04 CST

On Sun, Feb 24, 2008 at 9:38 AM, <fouchni_at_uni-osnabrueck.de> wrote:
> Dear all,

dear f.,

> First of all I apology for resending my question to a mailing list and to
> individuals. I am new in the field and didn't know how things work. Coming

there is nothing bad about not knowing things. happens to everybody. but
particularly as a researcher you should know that repeating an experiment
without modifications rarely teaches you anything new. there are actually
webpages with explanations of how to ask for help, with specific focus on
open source projects where most of the support is done voluntarily, so
that there are different "rules" on how people react, which have to be taken
into account to get a response. see e.g. the texts at:

http://freshmeat.net/articles/view/149/
and
http://www.catb.org/~esr/faqs/smart-questions.html

...and i personally would apreciate it when people identify themselves
(properly) with name and affiliation and give a little bit of background for
what they need the help for. it is _so_ much easier to answer to somebody
that appears as a real person (and especially not a generic gmail/yahoo/hotmail
account) with a context. when you ask for help in person you usually introduce
yourself and tell a little bit about what you do or want to do as well, right?

thanks,
    axel.

> back to my former question, I have a pdb file for a given structure
> (protein), and I would like to replace one or two residues in the
> structure with unkonwn residue. So how shall I add the unknown residue to
> residue library in VMD? My second question is how in general one can build

please note, that VMD is primarily a visualization and analysis tool and
not a molecular editor. in fact VMD itself has no knowledge about what
a specific residue should look like. if you'd change a pdb file so that a
lysine had the residue code of a glycine, VMD would for the most part
"believe" it and not notice the difference.

cheers,
     axel.

> a new residue (unsual residue)?
>
>
> Best regards,
> F. Ouchni
>
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.