Re: [PyMOL] deleting residues

[Tsjerk W. <ts...@gm...>]

Hi Orla,

You're not making clear what kind of effects you want to investigate.
Basically, it is possible to delete amino acids using pymol, but you
could as well use a text editor. If the purpose is to have a 'correct'
starting structure for further study (e.g. MD simulation), it's
unlikely to work. You won't know whether the result is reasonable
enough. Initially, you will create a long bond, which you might fix up
with an energy minimizer, but this is likely to screw up the structure
anyway. This said, if the residue(s) you want to delete are located in
an extended loop, you could probably get away with it, and yes, you
can do such modeling in Pymol.

Hope it helps,

Tsjerk

On 8/29/06, Orla O'Sullivan <Orl...@te...> wrote:
>
>
>
>
>
>
> Hi
>
>
>
> I have a PDB file and I want to look at the effects of deleting certain
> amino acids on the structure. Is this possible in pymol??
>
>
>
> Orla
>
> Dr. Orla O'Sullivan
>
> Research Officer
>
> Teagasc
>
> Moorepark Food Research Centre
>
> Fermoy
>
> Co. Cork
>
> Ireland
>
> Phone: 353 25 42344
>
> Fax: 353 25 42340
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336