 |
 |
I agree. We have encountered refinement problems similar to those Ed describes for models with mixtures of modified cysteine species, which is a fairly common occurrence. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 [log in to unmask] On 2/6/19, 11:19 AM, "CCP4 bulletin board on behalf of Palm, Gottfried" <[log in to unmask] on behalf of [log in to unmask]> wrote: >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 >[log in to unmask] >(214) 645-6383 (phone) >(214) 645-6353 (fax) > > >On Feb 6, 2019, at 1:36 AM, >[log in to unmask] <mailto:[log in to unmask]> 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:[log in to unmask]] Im Auftrag von Edwin > Pozharski >Gesendet: Montag, 4. Februar 2019 22:35 >An: [log in to unmask] >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 ><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX >5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=5 >33Wexf2P2dxZ7xNYAOkGTAhejw65fhzx7fdVjiaqR0&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 ><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNs >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=z >HHa24Rlcdaox9pZZIjljseiE2AQTGv-e_KUIaDRXUw&s=chhoO7n1Hhssuu6CKe06ss2fRhG9H >XDzqRBECM8y4Kc&e=> > > > > > >________________________________________ >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 ><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNs >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=z >HHa24Rlcdaox9pZZIjljseiE2AQTGv-e_KUIaDRXUw&s=chhoO7n1Hhssuu6CKe06ss2fRhG9H >XDzqRBECM8y4Kc&e=> > > > >________________________________________ >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c >gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNs >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=z >HHa24Rlcdaox9pZZIjljseiE2AQTGv-e_KUIaDRXUw&s=chhoO7n1Hhssuu6CKe06ss2fRhG9H >XDzqRBECM8y4Kc&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1