Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this. Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file. Thanks, Kirk -------- Kirk Moldoff www.galeriekirk.com 609-252-9479
Hi Kirk, Looking at the information for 3ALQ at the RCSB: <http://www.rcsb.org/pdb/explore/explore.do?structureId=3alq> …I see that chains A-F are TNF and chains R-W are TNFR. There are multiple ways to skin a cat, but for example, you could delete all the TNF chains with command: delete :.a-f General documentation on command-line specification in Chimera: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 27, 2013, at 3:59 PM, Kirk Moldoff <kmoldoff@verizon.net> wrote:
Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this.
Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file.
Thanks,
Kirk -------- Kirk Moldoff www.galeriekirk.com 609-252-9479
Sorry Everyone, accidentally hit reply, not reply all when sending Kirk my reply. Sorry for the double e-mail Kirk. Hey Kirk, Looking at the PDB.org information for the ID you stated (3ALQ) chains A, B, C, D, E, F are TNF and chains R, S, T, U, V, W are TNFR. Select each of the TNF chains one at a time under the select menu) and delete it, then move on to the next. When all are deleted you should just have the TNFR that you can save as a PDB! Hope that helps, Peter On 30/09/2013 1:28 PM, Kirk Moldoff wrote: Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this. Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file. Thanks, Kirk -------- Kirk Moldoff www.galeriekirk.com<http://www.galeriekirk.com> 609-252-9479
participants (3)
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Elaine Meng -
Kirk Moldoff -
Peter Murphy