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 > *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_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
