Hi Keitaro Perfect!
Thanks, that's great. Cheers -- Ian On Wed, 2 Dec 2020 at 22:31, Keitaro Yamashita <kyamash...@mrc-lmb.cam.ac.uk> wrote: > Dear Ian, > > For the moment in Refmac5 we need to use insertion codes to handle > microheterogeneity. LINKR records are also needed in the header. So > 7a5v.pdb should be changed like this: > > 954a955,957 > > LINKR THR A 279 LYS A 279A > gap > > LINKR C VAL A 278 N LYS A 279A > TRANS > > LINKR C THR A 279 N ALA A 280 > TRANS > 957c960 > < CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 > --- > > CRYST1 292.212 292.212 292.212 90.00 90.00 90.00 P 1 > > 3332,3347c3335,3350 > < 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 > --- > > ATOM 2354 N THR A 279 138.241 168.068 154.050 0.50 27.65 > N > > ATOM 2355 CA THR A 279 136.909 167.684 153.607 0.50 28.45 > C > > ATOM 2356 C THR A 279 135.937 167.731 154.799 0.50 31.92 > C > > ATOM 2357 O THR A 279 136.426 167.682 155.949 0.50 32.52 > O > > ATOM 2358 CB THR A 279 136.906 166.273 153.009 0.50 27.04 > C > > ATOM 2359 OG1 THR A 279 137.119 165.333 154.066 0.50 28.59 > O > > ATOM 2360 CG2 THR A 279 137.957 166.077 151.931 0.50 27.69 > C > > ATOM 2361 N LYS A 279A 138.238 168.081 154.020 0.50 32.20 > N > > ATOM 2362 CA LYS A 279A 136.870 167.701 153.585 0.50 36.51 > C > > ATOM 2363 C LYS A 279A 135.930 167.793 154.787 0.50 38.18 > C > > ATOM 2364 O LYS A 279A 136.377 168.014 155.910 0.50 42.23 > O > > ATOM 2365 CB LYS A 279A 136.887 166.298 152.984 0.50 40.70 > C > > ATOM 2366 CG LYS A 279A 137.909 166.091 151.872 0.50 46.05 > C > > ATOM 2367 CD LYS A 279A 138.177 164.645 151.591 0.50 50.67 > C > > ATOM 2368 CE LYS A 279A 139.166 164.047 152.568 0.50 59.69 > C > > ATOM 2369 NZ LYS A 279A 140.515 163.892 151.967 0.50 59.05 > N > > We deposited the PDB file that could be handled by Refmac5, but > insertion code was replaced with alt loc code in the annotation > process. > > Please also note that the NCS constraint function with evaluation of > nonbonded interactions etc will be available in the next update. > > Best regards, > Keitaro > > On 2020/12/02 21:41, Ian Tickle wrote: > > > > Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra > atoms in LYS). > > > > Strangely the error message is now repeated 91 times, even though there > are only 16 atoms (7+9) in the 2 residues: previously I only got the > message once ! > > > > Guess I must have imagined that it worked - it's called 'expectation > bias' ! > > > > Thanks anyway. > > > > -- Ian > > > > > > On Wed, 2 Dec 2020 at 18:34, Eleanor Dodson < > 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk <mailto: > 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: > > > > 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 <mailto: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 <mailto: > CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Ian > > > Tickle > > > Sent: Wednesday, December 2, 2020 15:02 > > > To: CCP4BB@JISCMAIL.AC.UK <mailto: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 < > 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 > <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 > <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ < > 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 < > 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 < > 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/
