Only a hunch but this works: ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O
ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65 N ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N In case 1 OD1 A is immediately followed bu OD1B In second case - all As listed then all Bs Eleanor On Wed, 2 Dec 2020 at 14:34, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Hi Ian, > > AFAIK there is no clean solution for this and I imagine this problem goes > very deep into the internal representation of the model in REFMAC. That > said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a > solution would be very welcome. > > Cheers, > Robbie > > > -----Original Message----- > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Ian > > Tickle > > Sent: Wednesday, December 2, 2020 15:02 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] Refmac not handling microheterogeneity? > > > > > > Dear All > > > > I just downloaded a PDB file (7A5V) from the EBI server, tried to run > Refmac > > on it and got the error: > > > > ERROR: in chain A residue: 279 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 ===> Error: > > Problem with coordinate file > > > > > > and indeed residue A279 has: > > > > ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65 > N > > > > and > > ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 > N > > and the same for all the other atoms in the residues. > > > > Searching the CCP4BB archives for "microheterogeneity" I see that this > has > > been discussed before and apparently it should "just work" if there are > alt > > atom indicators (check) and occupancies add up to <= 1 (check). I must > say I > > also was of the impression that it "just worked" so I'm a bit confused > now > > why it doesn't. > > > > Version info: > > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS" > > ### CCP4 7.1.008: Refmac version 5.8.0267 : 24/08/20## > > > > Is there some other hack I need to do to get it to work? > > > > Cheers > > > > -- Ian > > > > > > > > > > ________________________________ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
