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 <orla.osulli...@teagasc.ie> 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 PyMOL-users@lists.sourceforge.net 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
