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 <eleanor.dod...@york.ac.uk> 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 <wendy.of...@york.ac.uk> 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 <eleanor.dod...@york.ac.uk> >> 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.. >>> >>> >>> 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..) * >>> >>> *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 atoms to 5211 atoms. >>> Atom I Atom J Dij Sym 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 atoms to 9962 atoms. >>> Atom I Atom J Dij Sym 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&A=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/
