Re: [ccp4bb] Refmac not handling microheterogeneity?
; 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>> 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:
Re: [ccp4bb] Refmac not handling microheterogeneity?
5.910 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 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 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=1
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Re: [ccp4bb] Refmac not handling microheterogeneity?
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 < 176a9d5ebad7-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 > 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 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=1 >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Refmac not handling microheterogeneity?
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 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 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=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/
Re: [ccp4bb] Refmac not handling microheterogeneity?
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 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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[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=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/
