Re: [COOT] mon_lib_list.cif?
On 26/05/10 16:01, Scott Classen wrote: If I inspect the residue by looking at residue info I see that the atom names now have * instead of ' and the phosphate oxygens are O1P O2P instead of OP1 OP2. You are right of course, I'd forgotten how much Coot munges it into to make it match the dictionary. On 02/06/10 20:23, Scott Classen wrote: Just to reiterate When coot (0.6.2-pre-1 Miramar (revision 2965) ) imports a DNA with PDB v3 atom/residue names it converts them to v2 atom/residue names... except for the C7 of Thymidine which remains C7 instead of being renamed C5M. Yes indeed - this was mentioned a short while ago on the Phenix list. I think I'll add a temporary fix to do this renaming. The right way (as Phenix does it, I believe) is to the fix the dictionary to match the model, not the other way round. Paul.
Re: [COOT] mon_lib_list.cif?
Well, I think I can make a guess. Having been the target of a great deal of whingeing at the CCP4 developers meeting for hydrogen naming being in a mess (albeit not of his making), Paul finally caved in and agreed to do the wrong thing and kludge it in coot. Unfortunately it is now broken for the rest of the world. Is that fair, Paul? Scott Classen wrote: Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in. help, Scott ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~
Re: [COOT] mon_lib_list.cif?
Failure to read for comprehension. Sorry, wrong problem, ignore me. Kevin Cowtan wrote: Well, I think I can make a guess. Having been the target of a great deal of whingeing at the CCP4 developers meeting for hydrogen naming being in a mess (albeit not of his making), Paul finally caved in and agreed to do the wrong thing and kludge it in coot. Unfortunately it is now broken for the rest of the world. Is that fair, Paul? Scott Classen wrote: Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in. help, Scott ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~
Re: [COOT] mon_lib_list.cif?
Hi Scott, Congratulations for being up to date with you pre-release version. AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad, Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear to me what your custom cif files contain. Coot renames residue name to match the dictionary. I'd be very surprised indeed if Coot changed the atom names (as you said it did). The Right Way, it seems to me, to fix this, is to on-the-fly change the dictionary identifiers to the PDB standard (this is what I believe Phenix does). This update is tentatively scheduled for 0.8. For the moment though, for handling cif/dictionary/atom-naming convention problems with Coot, I recommend the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: COOT@JISCMAIL.AC.UK Subject: mon_lib_list.cif? Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in.
Re: [COOT] mon_lib_list.cif?
Hi Paul, here is one representative DNA base from my input PDB: HETATM 2795 PDT D 3 35.132 -34.748 -8.254 1.00 72.83 P HETATM 2796 OP1 DT D 3 34.082 -34.846 -9.292 1.00 80.59 O HETATM 2797 OP2 DT D 3 35.991 -33.545 -8.152 1.00 69.11 O HETATM 2798 O5' DT D 3 34.440 -34.961 -6.827 1.00 73.70 O HETATM 2799 C5' DT D 3 33.523 -36.031 -6.683 1.00 66.16 C HETATM 2800 C4' DT D 3 33.012 -36.178 -5.257 1.00 60.11 C HETATM 2801 O4' DT D 3 34.023 -36.716 -4.374 1.00 60.33 O HETATM 2802 C3' DT D 3 32.463 -34.922 -4.587 1.00 59.89 C HETATM 2803 O3' DT D 3 31.064 -35.096 -4.608 1.00 58.99 O HETATM 2804 C2' DT D 3 33.001 -34.977 -3.156 1.00 60.10 C HETATM 2805 C1' DT D 3 33.652 -36.352 -3.066 1.00 61.60 C HETATM 2806 N1 DT D 3 34.891 -36.374 -2.271 1.00 63.31 N HETATM 2807 C2 DT D 3 34.908 -37.067 -1.086 1.00 62.46 C HETATM 2808 N3 DT D 3 36.105 -37.034 -0.423 1.00 65.81 N HETATM 2809 C4 DT D 3 37.259 -36.396 -0.825 1.00 69.93 C HETATM 2810 C5 DT D 3 37.168 -35.687 -2.084 1.00 67.04 C HETATM 2811 C6 DT D 3 36.003 -35.711 -2.741 1.00 64.52 C HETATM 2812 O2 DT D 3 33.940 -37.659 -0.647 1.00 63.45 O HETATM 2813 O4 DT D 3 38.280 -36.444 -0.147 1.00 72.00 O HETATM 2814 C7 DT D 3 38.347 -34.949 -2.642 1.00 65.55 C If I inspect the residue by looking at residue info I see that the atom names now have * instead of ' and the phosphate oxygens are O1P O2P instead of OP1 OP2. Oddly C7 remains C7? (which I believe is C5M or somesuch in the version 2 atom names) When I save the coordinates from coot they look like this: HETATM 2795 PTd D 3 35.132 -34.748 -8.254 1.00 72.83 P HETATM 2796 O1P Td D 3 34.082 -34.846 -9.292 1.00 80.59 O HETATM 2797 O2P Td D 3 35.991 -33.545 -8.152 1.00 69.11 O HETATM 2798 O5* Td D 3 34.440 -34.961 -6.827 1.00 73.70 O HETATM 2799 C5* Td D 3 33.523 -36.031 -6.683 1.00 66.16 C HETATM 2800 C4* Td D 3 33.012 -36.178 -5.257 1.00 60.11 C HETATM 2801 O4* Td D 3 34.023 -36.716 -4.374 1.00 60.33 O HETATM 2802 C3* Td D 3 32.463 -34.922 -4.587 1.00 59.89 C HETATM 2803 O3* Td D 3 31.064 -35.096 -4.608 1.00 58.99 O HETATM 2804 C2* Td D 3 33.001 -34.977 -3.156 1.00 60.10 C HETATM 2805 C1* Td D 3 33.652 -36.352 -3.066 1.00 61.60 C HETATM 2806 N1 Td D 3 34.891 -36.374 -2.271 1.00 63.31 N HETATM 2807 C2 Td D 3 34.908 -37.067 -1.086 1.00 62.46 C HETATM 2808 N3 Td D 3 36.105 -37.034 -0.423 1.00 65.81 N HETATM 2809 C4 Td D 3 37.259 -36.396 -0.825 1.00 69.93 C HETATM 2810 C5 Td D 3 37.168 -35.687 -2.084 1.00 67.04 C HETATM 2811 C6 Td D 3 36.003 -35.711 -2.741 1.00 64.52 C HETATM 2812 O2 Td D 3 33.940 -37.659 -0.647 1.00 63.45 O HETATM 2813 O4 Td D 3 38.280 -36.444 -0.147 1.00 72.00 O HETATM 2814 C7 Td D 3 38.347 -34.949 -2.642 1.00 65.55 C I can send the custom cif file if you'd like. Essentially I've just updated the atom names and * to ' etc for the mon_lib_list.cif, AD.cif, CD.cif, GD.cif, and TD.cif files. Thanks, Scott On May 26, 2010, at 2:46 AM, Paul Emsley wrote: Hi Scott, Congratulations for being up to date with you pre-release version. AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad, Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear to me what your custom cif files contain. Coot renames residue name to match the dictionary. I'd be very surprised indeed if Coot changed the atom names (as you said it did). The Right Way, it seems to me, to fix this, is to on-the-fly change the dictionary identifiers to the PDB standard (this is what I believe Phenix does). This update is tentatively scheduled for 0.8. For the moment though, for handling cif/dictionary/atom-naming convention problems with Coot, I recommend the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: COOT@JISCMAIL.AC.UK Subject: mon_lib_list.cif? Hi all, I just
Re: [COOT] mon_lib_list.cif?
Hi all, My work flow is between coot and phenix.refine using only PDB version 3 DNA atom/res names. Currently my temporary work around is to do a global substitution using vi. Assuming your DNA is chain D then the following 2 lines entered at the command line will update the dna_from_coot.pdb file to version 3 happiness. vim -c argdo %s/ Gd D/ DG D/ge | %s/ Td D/ DT D/ge | %s/ Ad D/ DA D/ge | %s/ Cd D/ DC D/g | %s/O1P/OP1/ge | %s/O2P/OP2/ge | %s/C5M/C7 /ge | update dna_from_coot.pdb vim -c argdo %s/ O5\*/ O5'/ge | %s/ C5\*/ C5'/ge | %s/ C4\*/ C4'/ge | %s/ O4\*/ O4'/ge | %s/ C1\*/ C1'/ge | %s/ C2\*/ C2'/ge | %s/ C3\*/ C3'/ge | %s/ O3\*/ O3'/ge | update dna_from_coot.pdb Scott On May 26, 2010, at 2:46 AM, Paul Emsley wrote: Hi Scott, Congratulations for being up to date with you pre-release version. AD, CD, GD and TD are the filenames that Refmac uses to hold restraints for Ad, Cd, Gd and Td. The PDB standard names are DA, DC, DG and TD so it is not clear to me what your custom cif files contain. Coot renames residue name to match the dictionary. I'd be very surprised indeed if Coot changed the atom names (as you said it did). The Right Way, it seems to me, to fix this, is to on-the-fly change the dictionary identifiers to the PDB standard (this is what I believe Phenix does). This update is tentatively scheduled for 0.8. For the moment though, for handling cif/dictionary/atom-naming convention problems with Coot, I recommend the remediator. If Coot is really renaming the atoms (other than the coventional hydrogen name de-mangling), I'd like to know about it of course. Paul. From: Scott Classen [sclas...@lbl.gov] Sent: 25 May 2010 19:16 To: Paul Emsley; William Scott Cc: COOT@JISCMAIL.AC.UK Subject: mon_lib_list.cif? Hi all, I just updated to 0.6.2-pre-1 (build 2965) via fink I am using the PDB v3 atom names for DNA so I copied over my custom cif files to replace: /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif /sw/share/coot/lib/data/monomers/a/AD.cif /sw/share/coot/lib/data/monomers/c/CD.cif /sw/share/coot/lib/data/monomers/g/GD.cif /sw/share/coot/lib/data/monomers/t/TD.cif coot fires up OK. no complaints about the cif files, but coot is renaming my DNA atoms to version 2 atom names when it reads the PDB in.
