The situation might not be so rare, if you consider 50% Lys and 50% Acetyl-Lys or other post-translational modifications. Gottfried
On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote: If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the alternative residue is a Phe, then it would be ALEU and BPHE, both residues would have the same residue number, and reset the occupancies to fractions that sum to 1.0. Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 6, 2019, at 1:36 AM, herman.schreu...@sanofi.com wrote: Dear Edwin, I do not know whether your question has been answered already, but the answer is simple: you have to define alternative conformations. Easiest is to generate them in coot with the “add alternate conformation” option in the right panel. You may have to delete the original unlabeled alternative conformation first though. Alternatively, if you want to keep the original coordinates, or if the alternative residue is different: say a Leu versus a Phe you can open the pdb file with an editor and generate the alternative conformation yourself: One of the residues gets an “A” in front of the residue name, e.g. ALEU, and the alternative residue a “B”, say BLEU. You also have to reset the occupancies to 0.5 for both conformations (or different fractions which add up to one). Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin Pozharski Gesendet: Montag, 4. Februar 2019 22:35 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names Belated happy 2019, everyone. For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same residue ID. Presented with a pdb file that has such feature, Refmac fails saying this ERROR: in chain A residue: 443 different residues have the same number There is an error in the input coordinate file At least one the chains has 2 residues with the same number Check above to see error ===> Error: Problem with coordinate file There are several ways of getting around this I can think of. Perhaps duplicate chain with strict NCS for all but the residue in question could work. Perhaps adding this residue as two separate chains and then adding enough LINK records to keep things in place could. Either solution here is inelegant and requires reformating pdb file back to sanity prior to deposition. Is there some way to allow different geometries for alternate conformers that is native to Refmac? Cheers, Ed. PS. I know that phenix.refine takes the mixed name pdb file straight up. I still want to be able to refine such structure with refmac (and buster, actually, but that's a question I already asked in the appropriate forum. Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse / ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 [1] ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ------------------------- UT Southwestern Medical Center The future of medicine, today. ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 Links: ------ [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=533Wexf2P2dxZ7xNYAOkGTAhejw65fhzx7fdVjiaqR0&s=3CLcdo1WJ40rHm6l4rs8gd7nqHBgf_cZbvJjRgUfgHg&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
