Hi Diana, At the risk of thread-jacking Ed’s question, yes, PHENIX handles this seamlessly for us as well. However, REFMAC5 doesn’t like this scenario, with or without alt. confs. or insertion codes. There are some models where I’d really like to use REFMAC5 for refining these mixed species models, and it’s not clear to me how to do so. It sounds like Ed is encountering similar issues. 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 mwilso...@unl.edu On 2/6/19, 11:32 AM, "CCP4 bulletin board on behalf of Diana Tomchick" <CCP4BB@JISCMAIL.AC.UK on behalf of diana.tomch...@utsouthwestern.edu> wrote: > > > >The scenario I presented earlier works like a charm in refinement with >the Phenix program suite. For example, I have used it for both mixed >populations of ligands (e.g., AAMP and BADP) as well as phosphorylation >(ASER and BSEP). > > >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 11:19 AM, Edwin Pozharski <pozharsk...@gmail.com> >wrote: > >Herman, > > >thanks - however, it seems like I have poorly worded my question. I do >know how to generate alternate conformers, what the PDB ATOM record >format is etc. The point was that when I have alternate conformers that >carry the same residue ID but > different residue types, Refmac exits with the error. The question was >whether there is a "native" solution to this that does not include some >pdb file acrobatics (i.e. separating the alternative type into a separate >residue and enforcing connectivity using > elaborate LINK records). Based on what I see so far, there likely >isn't any such native option. Whether these situations are common enough >to warrant (possibly elaborate) software changes is a separate question. > > >Cheers, > > >Ed. > > >--- > >I don't know why the sacrifice didn't work. The science seemed so solid. > >Julien XIII, Lord of the Lemurs > > > > >On Wed, Feb 6, 2019 at 2:36 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 <mailto: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 ><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=DwMGaQ&c=Cu5g146wZdoqVuKpTNs >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=O >mNRrhhr7Mb_WHh0QNl3PVbuxGrr-RhpYEHPz9NvLzw&s=0kpfQ0LGuYj5DbX0812lLqo8JI_w9 >ydGDkb0X9pNMxs&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=DwMGaQ&c=Cu5g146wZdoqVuKpTNs >YHeFX_rg6kWhlkLF8Eft-wwo&r=pWFylCwRYnT2UZGAgJCqKaJCAAfFi00TZEWmZXJvhsA&m=O >mNRrhhr7Mb_WHh0QNl3PVbuxGrr-RhpYEHPz9NvLzw&s=0kpfQ0LGuYj5DbX0812lLqo8JI_w9 >ydGDkb0X9pNMxs&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
