VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 17 2012 - 11:11:00 CDT

On Thu, May 17, 2012 at 8:42 AM, P.-L. Chau <pc104_at_pasteur.fr> wrote:
> Thank you for your message.
>
>> VMD does what *you* ask it to do.
>>
>> [...]
>>
>> VMD is deliberately not trying to be too smart,
>> but rather relies on consistent input data.
>> so if you want scripts to work well, you have
>> to make sure that your selections match the
>> indicators that VMD uses. details on that should
>> all be listed in the user's guide.
>
> Could I ask you if you could possibly be a bit more specific on what I
> should be looking for, please? I have scoured the VMD user's guide, but
> have found precious little about splitting files for preparation for NAMD.
> Would there be some extra tutorial about splitting files and handling ATOM
> and HETATM in pdb files, please?

you are looking for *too* specific an answer.
a versatile tool like VMD cannot have tutorials
for every specific use case. there are too many.
also, you have to keep in mind that there are
often multiple way to do (almost) the same thing.
there is never just one answer.

so you have to assemble the knowledge you
need from the components present. that
first means that you identify the specific cause
of your problems. from your description is is
apparent, that you don't fully understand
the details of the atomselect command, so
you have to make an effort to understand it better.

also, once you've read a file into VMD (and
that is what i already said) the distinction
between ATOM and HETATM records is gone.
this is a pdb file specific thing. so relying on
VMD to know about it is asking for too much.

that is what i meant with "software has no
common sense". you have to look for identifiers
that reliably work with the data that VMD can
extract.

most the VMD internal heuristics are explained
in the description of the predefined atom
selection macros. understanding those will
help you for realize why VMD sometimes
guesses right and sometimes wrong.
to make it do the right thing, you have to
make sure that you provide the adequate
information and follow the expected conventions.

cheers,
    axel.

> Thank you very much!
>
> P-L Chau
>
> email: pc104_at_pasteur.fr
> Bioinformatique Structurale
> CNRS URA 2185
> Institut Pasteur
> 75724 Paris
> France
> tel: +33 1 45688546
> fax: +33 1 45688719
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.