Re: [ccp4bb] Phenix/refmac incompatibility?
Robbie joosten says it is fixed - a bug seen by pdb- redo from an old version of Phoenix. Message him for more detail... cheers Eleanor On Fri, 31 Dec 2021 at 22:27, Pavel Afonine wrote: > Hi All, > who produced this file? If phenix.refine added water with chain S given > that protein chains named S were already in that model, then it is a bug > that I need to fix. > Cheers, > Pavel > > On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> I am not sure whether I have this straight but someone has sent a pdb >> file from phenix refinement with these atoms in the pdb file.. >> >> ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25 >> N >> ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78 >> C >> ATOM 5582 C GLY S 18 37.048 43.211 58.097 1.00 73.20 >> C >> ATOM 5583 O GLY S 18 37.043 42.043 57.734 1.00 74.31 >> O >> ATOM 5584 N SER S 19 36.992 43.568 59.375 1.00 75.40 >> N >> ... >> >> HETATM11068 O HOH S 16 68.933 60.684 119.353 1.00 32.35 >> O >> HETATM11069 O HOH S 17 17.772 20.649 91.306 1.00 40.79 >> O >> HETATM11070 O HOH S 18 23.684 50.229 65.614 1.00 41.00 >> O >> HETATM11071 O HOH S 19 45.488 71.114 105.890 1.00 51.50 >> O >> >> Then REFMAC gets upset because "residue" S 18 appears twice.. >> >> Doesnt PHENIX worry about this? or has the user edits these HOH atoms >> into the file? >> >> And what should we do about it >> Eleanor >> >> >> >> -- >> >> 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] Phenix/refmac incompatibility?
Hi All, who produced this file? If phenix.refine added water with chain S given that protein chains named S were already in that model, then it is a bug that I need to fix. Cheers, Pavel On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > I am not sure whether I have this straight but someone has sent a pdb file > from phenix refinement with these atoms in the pdb file.. > > ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25 > N > ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78 > C > ATOM 5582 C GLY S 18 37.048 43.211 58.097 1.00 73.20 > C > ATOM 5583 O GLY S 18 37.043 42.043 57.734 1.00 74.31 > O > ATOM 5584 N SER S 19 36.992 43.568 59.375 1.00 75.40 > N > ... > > HETATM11068 O HOH S 16 68.933 60.684 119.353 1.00 32.35 > O > HETATM11069 O HOH S 17 17.772 20.649 91.306 1.00 40.79 > O > HETATM11070 O HOH S 18 23.684 50.229 65.614 1.00 41.00 > O > HETATM11071 O HOH S 19 45.488 71.114 105.890 1.00 51.50 > O > > Then REFMAC gets upset because "residue" S 18 appears twice.. > > Doesnt PHENIX worry about this? or has the user edits these HOH atoms into > the file? > > And what should we do about it > Eleanor > > > > -- > > 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] Phenix/refmac incompatibility?
Thanks Robbie - so we dont need to bother much about it... E On Fri, 31 Dec 2021 at 15:21, Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > I was going to suggest returning to this topic in 3 months time. It has > that sort of quality ;-? > > > Sent from ProtonMail mobile > > > > Original Message > On 31 Dec 2021, 15:17, Robbie Joosten < robbie_joos...@hotmail.com> wrote: > > > Hi Eleanor, > > This seems to be a caused by a bug in an older version of Phenix. We used > to see quite a few examples of this on the PDB-REDO server, but not > recently. Renumbering is the only solution I'm afraid. > > Cheers, > Robbie > > On 30 Dec 2021 20:05, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > I am not sure whether I have this straight but someone has sent a pdb file > from phenix refinement with these atoms in the pdb file.. > > ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25 > N > ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78 > C > ATOM 5582 C GLY S 18 37.048 43.211 58.097 1.00 73.20 > C > ATOM 5583 O GLY S 18 37.043 42.043 57.734 1.00 74.31 > O > ATOM 5584 N SER S 19 36.992 43.568 59.375 1.00 75.40 > N > ... > > HETATM11068 O HOH S 16 68.933 60.684 119.353 1.00 32.35 > O > HETATM11069 O HOH S 17 17.772 20.649 91.306 1.00 40.79 > O > HETATM11070 O HOH S 18 23.684 50.229 65.614 1.00 41.00 > O > HETATM11071 O HOH S 19 45.488 71.114 105.890 1.00 51.50 > O > > Then REFMAC gets upset because "residue" S 18 appears twice.. > > Doesnt PHENIX worry about this? or has the user edits these HOH atoms into > the file? > > And what should we do about it > Eleanor > > > > -- > > 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 > > -- > > 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] Phenix/refmac incompatibility?
I was going to suggest returning to this topic in 3 months time. It has that sort of quality ;-? Sent from ProtonMail mobile Original Message On 31 Dec 2021, 15:17, Robbie Joosten wrote: > Hi Eleanor, > > This seems to be a caused by a bug in an older version of Phenix. We used to > see quite a few examples of this on the PDB-REDO server, but not recently. > Renumbering is the only solution I'm afraid. > > Cheers, > Robbie > > On 30 Dec 2021 20:05, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> I am not sure whether I have this straight but someone has sent a pdb file >> from phenix refinement with these atoms in the pdb file.. >> >> ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25 N >> ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78 C >> ATOM 5582 C GLY S 18 37.048 43.211 58.097 1.00 73.20 C >> ATOM 5583 O GLY S 18 37.043 42.043 57.734 1.00 74.31 O >> ATOM 5584 N SER S 19 36.992 43.568 59.375 1.00 75.40 N >> ... >> >> HETATM11068 O HOH S 16 68.933 60.684 119.353 1.00 32.35 O >> HETATM11069 O HOH S 17 17.772 20.649 91.306 1.00 40.79 O >> HETATM11070 O HOH S 18 23.684 50.229 65.614 1.00 41.00 O >> HETATM11071 O HOH S 19 45.488 71.114 105.890 1.00 51.50 O >> >> Then REFMAC gets upset because "residue" S 18 appears twice.. >> >> Doesnt PHENIX worry about this? or has the user edits these HOH atoms into >> the file? >> >> And what should we do about it >> Eleanor >> >> >> >> --- >> >> 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 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] Phenix/refmac incompatibility?
Hi Eleanor,This seems to be a caused by a bug in an older version of Phenix. We used to see quite a few examples of this on the PDB-REDO server, but not recently. Renumbering is the only solution I'm afraid.Cheers,RobbieOn 30 Dec 2021 20:05, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:I am not sure whether I have this straight but someone has sent a pdb file from phenix refinement with these atoms in the pdb file..ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25 NATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78 CATOM 5582 C GLY S 18 37.048 43.211 58.097 1.00 73.20 CATOM 5583 O GLY S 18 37.043 42.043 57.734 1.00 74.31 OATOM 5584 N SER S 19 36.992 43.568 59.375 1.00 75.40 N...HETATM11068 O HOH S 16 68.933 60.684 119.353 1.00 32.35 OHETATM11069 O HOH S 17 17.772 20.649 91.306 1.00 40.79 OHETATM11070 O HOH S 18 23.684 50.229 65.614 1.00 41.00 OHETATM11071 O HOH S 19 45.488 71.114 105.890 1.00 51.50 OThen REFMAC gets upset because "residue" S 18 appears twice..Doesnt PHENIX worry about this? or has the user edits these HOH atoms into the file?And what should we do about itEleanor 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
