Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
On 01/09/2023 17:40, Eleanor Dodson wrote: Is that coot in the latest ccp4 distribution? By "that" I presume you mean "Coot 0.9.8.92." No, it is not. Currently it is merely a twinkle in the developer's eye. I'll try to find some time next week to make a release. Paul. On Fri, 1 Sep 2023 at 17:37, Paul Emsley wrote: Dear Eleanor [snip] To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
Is that coot in the latest ccp4 distribution? On Fri, 1 Sep 2023 at 17:37, Paul Emsley wrote: > Dear Eleanor > > > On 01/09/2023 13:19, Eleanor Dodson wrote: > > *COOT problem first: or is it REFMAC ? * > REFMAC outputs coordinates in both pdb and cif format. They are > identical > *This model has ZN linked to CYSs etc..* > The PDB files provides the link records but the cif file does not. > > eleanor@wombat job_187 % grep -i link > Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb > LINK OE2 GLU A 338ZNZN A 701 1555 1555 > 2.020 > LINKRC2 DRG A 702 SG CYS A 417 > DRG-CYS > LINKR ZNZN A 701 SG CYS A 340 > ZN-CYS > LINKR ZNZN A 701 SG CYS A 417 > ZN-CYS > LINKR ZNZN A 701 SG CYS A 418 > ZN-CYS > > But the only mention of ZN in the cif format is the actual coordinate. > nolink definitions.. > > > The mmCIF format file as output by which program? As far as I can tell, > your talking about Refmac. > > > > > eleanor@wombat job_187 % grep -i zn > 181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif > HETATM 10117 ZN ZN . ZN A2 2 . . . 2.0627321 25.812978 > 14.7728311 68.493 ? ? ? ? ? +0 701 ZN A ZN 1 > > > > *There is also a di-sulphide mess. the cif output from COOT forces close > SG to form unwanted SSBONDS. (Of course this may only happen because the ZN > links are lost..) * > > > As mentioned earlier today in a related but different thread, this should > be fixed in 7e2518b1452f18d011db43b57210bce71cfa41e5. > > On 01/09/2023 13:35, Wendy Offen wrote: > > Yes, it is coordinated to the CYS residues. So maybe it does need to be > shown as having links > I was just confused because links for covalent bonds look the same as for > coordinations. > > > Yes - a Link should appear w̶i̶t̶h̶ ̶t̶h̶e̶ ̶M̶a̶s̶t̶e̶r̶ ̶S̶w̶o̶r̶d̶ as a > dotted line (even the the case of a Schiff base, for the record) - Coot > doesn't care about the bond type when representing a Link. > > > > *Here ..[snip]* > Is this comprehensible?? > > > Comprehensible enough for me to think that we would have a much more > productive exchange in the light of your using Coot-0.9.8.92 - which will > contain the above fix. > > > Regards, > > > Paul. > > > > -- > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
Dear Eleanor On 01/09/2023 13:19, Eleanor Dodson wrote: *COOT problem first: or is it REFMAC ? * REFMAC outputs coordinates in both pdb and cif format. They are identical *This model has ZN linked to CYSs etc..* The PDB files provides the link records but the cif file does not. eleanor@wombat job_187 % grep -i link Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb LINK OE2 GLU A 338 ZN ZN A 701 1555 1555 2.020 LINKR C2 DRG A 702 SG CYS A 417 DRG-CYS LINKR ZN ZN A 701 SG CYS A 340 ZN-CYS LINKR ZN ZN A 701 SG CYS A 417 ZN-CYS LINKR ZN ZN A 701 SG CYS A 418 ZN-CYS But the only mention of ZN in the cif format is the actual coordinate. nolink definitions.. The mmCIF format file as output by which program? As far as I can tell, your talking about Refmac. eleanor@wombat job_187 % grep -i zn 181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif HETATM 10117 ZN ZN . ZN A2 2 . . . 2.0627321 25.812978 14.772831 1 68.493 ? ? ? ? ? +0 701 ZN A ZN 1 *There is also a di-sulphide mess. the cif output from COOT forces close SG to form unwanted SSBONDS. (Of course this may only happen because the ZN links are lost..) * As mentioned earlier today in a related but different thread, this should be fixed in 7e2518b1452f18d011db43b57210bce71cfa41e5. On 01/09/2023 13:35, Wendy Offen wrote: Yes, it is coordinated to the CYS residues. So maybe it does need to be shown as having links I was just confused because links for covalent bonds look the same as for coordinations. Yes - a Link should appear w̶i̶t̶h̶ ̶t̶h̶e̶ ̶M̶a̶s̶t̶e̶r̶ ̶S̶w̶o̶r̶d̶ as a dotted line (even the the case of a Schiff base, for the record) - Coot doesn't care about the bond type when representing a Link. * * *Here ..[snip]* Is this comprehensible?? Comprehensible enough for me to think that we would have a much more productive exchange in the light of your using Coot-0.9.8.92 - which will contain the above fix. Regards, Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
Yes, it is coordinated to the CYS residues. So maybe it does need to be shown as having links I was just confused because links for covalent bonds look the same as for coordinations. W On Fri, 1 Sept 2023 at 13:31, Eleanor Dodson wrote: > But ZN IS coordinated to the CYS surely? and if you dont specify a LINK > refinement will apply VDW repulsion to keep the atoms apart?? > > E > > On Fri, 1 Sept 2023 at 13:30, Wendy Offen wrote: > >> Just to clarify, I don't think there should be links from the Zn to the >> cysteines. The Zn should just be a coordinated metal. >> But there is a covalent link from DRG C2 to SG Cys417 >> >> Thanks >> >> Wendy >> >> On Fri, 1 Sept 2023 at 13:19, Eleanor Dodson >> wrote: >> >>> *COOT problem first: or is it REFMAC ? * >>> REFMAC outputs coordinates in both pdb and cif format. They are >>> identical >>> *This model has ZN linked to CYSs etc..* >>> The PDB files provides the link records but the cif file does not. >>> >>> eleanor@wombat job_187 % grep -i link >>> Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb >>> LINK OE2 GLU A 338ZNZN A 701 1555 1555 >>> 2.020 >>> LINKRC2 DRG A 702 SG CYS A 417 >>> DRG-CYS >>> LINKR ZNZN A 701 SG CYS A 340 >>> ZN-CYS >>> LINKR ZNZN A 701 SG CYS A 417 >>> ZN-CYS >>> LINKR ZNZN A 701 SG CYS A 418 >>> ZN-CYS >>> >>> But the only mention of ZN in the cif format is the actual coordinate. >>> nolink definitions.. >>> >>> >>> eleanor@wombat job_187 % grep -i zn >>> 181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >>> HETATM 10117 ZN ZN . ZN A2 2 . . . 2.0627321 25.812978 >>> 14.7728311 68.493 ? ? ? ? ? +0 701 ZN A ZN 1 >>> >>> >>> *There is also a di-sulphide mess. the cif output from COOT forces close >>> SG to form unwanted SSBONDS. (Of course this may only happen because the ZN >>> links are lost..) * >>> >>> *Here are the correct SG bonds as listed by distang - only contacts to >>> the ZN* >>> *(Note there is a file name problem too. distang on the Mac wont accept >>> a file name with spaces in it...) )* >>> wombat:job_187 eleanor$ cp >>> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/Job*format-coot-0allref.pdb >>> junk.pdb >>> >>> ### >>> ### >>> ### >>> ### CCP4 8.0.015: DISTANG version 8.0.015 : ## >>> ### >>> >>> Logical name: XYZIN File name: junk.pdb >>> PDB file is being opened on unit 1 for INPUT. >>> >>> >>> radi S 1.2 Zn 1.5 >>> Data line--- radi S 1.2 Zn 1.5 >>> end >>> Data line--- end >>> number of atoms input 5211 >>> Searching from 5211 atomsto 5211 atoms. >>> Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) >>> av_bi+bj >>> >>> >>> *C 340 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 >>> 69.95 C 417 SG A Z 701 ZN A 2.335 X,Y,Z 1.00 >>> 71.32 C 418 SG A Z 701 ZN A 2.325 X,Y,Z >>> 1.00 69.31* >>> >>> >>> >>> >>> And the same calculation after coot refinement of the cif coordinates... >>> >>> wombat:job_187 eleanor$ distang xyzin >>> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >>> >>> Logical name: XYZIN File name: >>> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >>> radi S 1.5 ZN 1.5 >>> Data line--- radi S 1.5 ZN 1.5 >>> end >>> Data line--- end >>> Searching from 9962 atomsto 9962 atoms. >>> Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) >>> av_bi+bj >>> * C 340 SG A C 418 SG A 2.051 X,Y,Z 1.00 >>> 70.77* >>> C 340 SG A Z 701 ZN A 2.332 X,Y,Z 1.00 >>> 69.98 >>> >>> >>> * C 415 SG A C 417 SG A 2.010 X,Y,Z 1.00 >>> 78.92* >>> >>> >>> C 417 SG A C 415 SG A 2.010 X,Y,Z 1.00 >>> 78.92 >>> C 417 SG A Z 701 ZN A 2.373 X,Y,Z 1.00 >>> 71.32 >>> >>> >>> C 418 SG A C 340 SG A 2.051 X,Y,Z 1.00 >>> 70.77 >>> C 418 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 >>> 69.27 >>> >>> >>> Z 701 ZN A C 340 SG A 2.332 X,Y,Z 1.00 >>> 69.98 >>> Z 701 ZN A C 417 SG A 2.373 X,Y,Z 1.00 >>> 71.32 >>> Z 701 ZN A C 418 SG A 2.324 X,Y,Z 1.00 >>> 69.27 >>> >>> >>> Is this comprehensible?? >>> Eleanor >>> >>> >>>
Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
Just to clarify, I don't think there should be links from the Zn to the cysteines. The Zn should just be a coordinated metal. But there is a covalent link from DRG C2 to SG Cys417 Thanks Wendy On Fri, 1 Sept 2023 at 13:19, Eleanor Dodson wrote: > *COOT problem first: or is it REFMAC ? * > REFMAC outputs coordinates in both pdb and cif format. They are identical > *This model has ZN linked to CYSs etc..* > The PDB files provides the link records but the cif file does not. > > eleanor@wombat job_187 % grep -i link > Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb > LINK OE2 GLU A 338ZNZN A 701 1555 1555 > 2.020 > LINKRC2 DRG A 702 SG CYS A 417 > DRG-CYS > LINKR ZNZN A 701 SG CYS A 340 > ZN-CYS > LINKR ZNZN A 701 SG CYS A 417 > ZN-CYS > LINKR ZNZN A 701 SG CYS A 418 > ZN-CYS > > But the only mention of ZN in the cif format is the actual coordinate. > nolink definitions.. > > > eleanor@wombat job_187 % grep -i zn > 181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif > HETATM 10117 ZN ZN . ZN A2 2 . . . 2.0627321 25.812978 > 14.7728311 68.493 ? ? ? ? ? +0 701 ZN A ZN 1 > > > *There is also a di-sulphide mess. the cif output from COOT forces close > SG to form unwanted SSBONDS. (Of course this may only happen because the ZN > links are lost..) * > > *Here are the correct SG bonds as listed by distang - only contacts to the > ZN* > *(Note there is a file name problem too. distang on the Mac wont accept a > file name with spaces in it...) )* > wombat:job_187 eleanor$ cp > /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/Job*format-coot-0allref.pdb > junk.pdb > > ### > ### > ### > ### CCP4 8.0.015: DISTANG version 8.0.015 : ## > ### > > Logical name: XYZIN File name: junk.pdb > PDB file is being opened on unit 1 for INPUT. > > > radi S 1.2 Zn 1.5 > Data line--- radi S 1.2 Zn 1.5 > end > Data line--- end > number of atoms input 5211 > Searching from 5211 atomsto 5211 atoms. > Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) > av_bi+bj > > > *C 340 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 > 69.95 C 417 SG A Z 701 ZN A 2.335 X,Y,Z 1.00 > 71.32 C 418 SG A Z 701 ZN A 2.325 X,Y,Z > 1.00 69.31* > > > > > And the same calculation after coot refinement of the cif coordinates... > > wombat:job_187 eleanor$ distang xyzin > /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif > > Logical name: XYZIN File name: > /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif > radi S 1.5 ZN 1.5 > Data line--- radi S 1.5 ZN 1.5 > end > Data line--- end > Searching from 9962 atomsto 9962 atoms. > Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) > av_bi+bj > * C 340 SG A C 418 SG A 2.051 X,Y,Z 1.00 > 70.77* > C 340 SG A Z 701 ZN A 2.332 X,Y,Z 1.00 > 69.98 > > > * C 415 SG A C 417 SG A 2.010 X,Y,Z 1.00 > 78.92* > > > C 417 SG A C 415 SG A 2.010 X,Y,Z 1.00 > 78.92 > C 417 SG A Z 701 ZN A 2.373 X,Y,Z 1.00 > 71.32 > > > C 418 SG A C 340 SG A 2.051 X,Y,Z 1.00 > 70.77 > C 418 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 > 69.27 > > > Z 701 ZN A C 340 SG A 2.332 X,Y,Z 1.00 > 69.98 > Z 701 ZN A C 417 SG A 2.373 X,Y,Z 1.00 > 71.32 > Z 701 ZN A C 418 SG A 2.324 X,Y,Z 1.00 > 69.27 > > > Is this comprehensible?? > Eleanor > > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] A COOT mess showing up at deposition - no cif links and auto (false) Di-sulphides formed
But ZN IS coordinated to the CYS surely? and if you dont specify a LINK refinement will apply VDW repulsion to keep the atoms apart?? E On Fri, 1 Sept 2023 at 13:30, Wendy Offen wrote: > Just to clarify, I don't think there should be links from the Zn to the > cysteines. The Zn should just be a coordinated metal. > But there is a covalent link from DRG C2 to SG Cys417 > > Thanks > > Wendy > > On Fri, 1 Sept 2023 at 13:19, Eleanor Dodson > wrote: > >> *COOT problem first: or is it REFMAC ? * >> REFMAC outputs coordinates in both pdb and cif format. They are >> identical >> *This model has ZN linked to CYSs etc..* >> The PDB files provides the link records but the cif file does not. >> >> eleanor@wombat job_187 % grep -i link >> Job*181:*Model*from*refinement*PDB*format-coot-0allref.pdb >> LINK OE2 GLU A 338ZNZN A 701 1555 1555 >> 2.020 >> LINKRC2 DRG A 702 SG CYS A 417 >> DRG-CYS >> LINKR ZNZN A 701 SG CYS A 340 >> ZN-CYS >> LINKR ZNZN A 701 SG CYS A 417 >> ZN-CYS >> LINKR ZNZN A 701 SG CYS A 418 >> ZN-CYS >> >> But the only mention of ZN in the cif format is the actual coordinate. >> nolink definitions.. >> >> >> eleanor@wombat job_187 % grep -i zn >> 181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >> HETATM 10117 ZN ZN . ZN A2 2 . . . 2.0627321 25.812978 >> 14.7728311 68.493 ? ? ? ? ? +0 701 ZN A ZN 1 >> >> >> *There is also a di-sulphide mess. the cif output from COOT forces close >> SG to form unwanted SSBONDS. (Of course this may only happen because the ZN >> links are lost..) * >> >> *Here are the correct SG bonds as listed by distang - only contacts to >> the ZN* >> *(Note there is a file name problem too. distang on the Mac wont accept a >> file name with spaces in it...) )* >> wombat:job_187 eleanor$ cp >> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/Job*format-coot-0allref.pdb >> junk.pdb >> >> ### >> ### >> ### >> ### CCP4 8.0.015: DISTANG version 8.0.015 : ## >> ### >> >> Logical name: XYZIN File name: junk.pdb >> PDB file is being opened on unit 1 for INPUT. >> >> >> radi S 1.2 Zn 1.5 >> Data line--- radi S 1.2 Zn 1.5 >> end >> Data line--- end >> number of atoms input 5211 >> Searching from 5211 atomsto 5211 atoms. >> Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) >> av_bi+bj >> >> >> *C 340 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 >> 69.95 C 417 SG A Z 701 ZN A 2.335 X,Y,Z 1.00 >> 71.32 C 418 SG A Z 701 ZN A 2.325 X,Y,Z >> 1.00 69.31* >> >> >> >> >> And the same calculation after coot refinement of the cif coordinates... >> >> wombat:job_187 eleanor$ distang xyzin >> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >> >> Logical name: XYZIN File name: >> /Users/eleanor/CCP4I2_PROJECTS/HypBA1-VBC75-AN6906/CCP4_JOBS/job_187/181_hypba1-vbc75-an6906_ciffile_prosmart_refmac.cif-coot-0ref2.cif >> radi S 1.5 ZN 1.5 >> Data line--- radi S 1.5 ZN 1.5 >> end >> Data line--- end >> Searching from 9962 atomsto 9962 atoms. >> Atom I Atom J DijSym TX TY TZ occ(i)*occ(j) >> av_bi+bj >> * C 340 SG A C 418 SG A 2.051 X,Y,Z 1.00 >> 70.77* >> C 340 SG A Z 701 ZN A 2.332 X,Y,Z 1.00 >> 69.98 >> >> >> * C 415 SG A C 417 SG A 2.010 X,Y,Z 1.00 >> 78.92* >> >> >> C 417 SG A C 415 SG A 2.010 X,Y,Z 1.00 >> 78.92 >> C 417 SG A Z 701 ZN A 2.373 X,Y,Z 1.00 >> 71.32 >> >> >> C 418 SG A C 340 SG A 2.051 X,Y,Z 1.00 >> 70.77 >> C 418 SG A Z 701 ZN A 2.324 X,Y,Z 1.00 >> 69.27 >> >> >> Z 701 ZN A C 340 SG A 2.332 X,Y,Z 1.00 >> 69.98 >> Z 701 ZN A C 417 SG A 2.373 X,Y,Z 1.00 >> 71.32 >> Z 701 ZN A C 418 SG A 2.324 X,Y,Z 1.00 >> 69.27 >> >> >> Is this comprehensible?? >> Eleanor >> >> >> To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
