Mark, You could always simply edit the pdb file (remove the trans option). Simply open up the pdb file in a text editor (gedit/notetab/wordpad) and delete the lines corresponding to the trans form. The pdb file (compare with the mol or mol2 files) is simple to edit manually. The others require connectivity etc to be edited.
The last pdb file I saw with an alt conf looked like this: ATOM 53 CG2AVAL A 6 -5.306 -11.323 22.865 0.50 11.50 A C ATOM 54 CG2BVAL A 6 -7.334 -10.108 21.413 0.50 12.94 A C ATOM 55 C VAL A 6 -8.805 -10.428 23.682 1.00 11.53 A C ATOM 56 O VAL A 6 -9.347 -11.540 23.573 1.00 12.73 A O Where the AVAL and BVal correspond to different orientations. Hope this helps _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: Mark Bostock [mailto:mjb...@cam.ac.uk] Sent: Saturday, 10 December 2011 10:26 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Changing ligand conformation I have a pdb file of a protein which contains a lysine residue bound to a ligand. The ligand has two conformations due to a cis/trans isomerisation. I have created a pdb file (also .mol and .mol2) of lysine attached to the cis form and would like to replace the lysine-ligand(trans) form which is currently in the protein structure with the lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis only gives me the option of standard amino acids and also does not remove the existing ligand. Many thanks, Mark. ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
