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>
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