Re: [ccp4bb] how to get mol files from PDB and restraint CIF?
The PDB format does not encode the bond orders (single, double, triple, aromatic bond) that are required to produce the correct format of input (SMILES / MOL / SDF / MOL2 / mmCIF) to Grade. This is particularly important if some or all H atoms are absent and/or the PDB co-ordinates have not been refined, as then the bond orders and H atom placement cannot always be reliably determined. I've seen several cases where the PDB automated deposition has placed H atoms incorrectly in a ligand and shown an incorrect chemical structure diagram even where the ligand has undergone refinement. Ideally of course it's up to the depositor to supply SMILES for new ligands to eliminate all doubt (this may now be a requirement). This is particularly a problem in the case of covalently-bound ligands because the bonding may differ between the free and bound ligands. The depositor will usually supply the SMILES for the free ligand but obviously one cannot assume the same bond orders and H atom placement for the bound ligand. For this reason the restraint dictionaries actually used in the refinement should always be supplied (this also makes validation much easier). Cheers -- Ian On Fri, 19 May 2023, 17:11 Tim Gruene, wrote: > Hi Frank, > > in line with Paul's comment, what is so apparent about openbabel not > doing the job? I use it frequently to generate the input from PDB to the > Grade-Server. > > Cheers, > Tim > > On Fri, 19 May 2023 10:28:32 +0100 Frank von Delft > wrote: > > > OpenBabel apparently does not. > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > > > 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] how to get mol files from PDB and restraint CIF?
Hi Frank, in line with Paul's comment, what is so apparent about openbabel not doing the job? I use it frequently to generate the input from PDB to the Grade-Server. Cheers, Tim On Fri, 19 May 2023 10:28:32 +0100 Frank von Delft wrote: > OpenBabel apparently does not. -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A 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/ pgpV4cstNO2ON.pgp Description: OpenPGP digital signature
Re: [ccp4bb] how to get mol files from PDB and restraint CIF?
On 19/05/2023 10:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF file used in refinement, and generate a .mol (or .sdf)
file?
Isn't this a bit of strange request? .sdf files are for coordinates, it
is not clear to me how they would encode restraint information (other
than simply minimizing the ligand of course (and if you are using the
monomer library it is likely that Refmac has done this for you)).
Here's how you convert a residue/ligand to an sdf using coot:
import coot
imol = coot.get_monomer("AMP")
coot.residue_to_sdf_file(imol, "A", 1, "", "AMP.sdf")
Paul.
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Re: [ccp4bb] how to get mol files from PDB and restraint CIF?
apologies for a brief note: mmCIF is the default for structural biology data and the ways to avoid its use are just improvisations leading to more improvisations. Bohdan, bs.structbio.org On 2023-05-19 11:48, Frank von Delft wrote: Really, no CIF needed? As far as I know, it's only in the CIF file that the precise atom identities can be found. You can infer them from the PDB lines, but that rather misses the point. Frank On 19/05/2023 10:42, Fred Vellieux wrote: Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://datascience.unm.edu/tomcat/biocomp/convert Sometimes the conversion doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my collaborator couldn't find them. Any pointers welcome. (To save us time.) Thanks! Frank 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/ 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] how to get mol files from PDB and restraint CIF?
Really, no CIF needed? As far as I know, it's only in the CIF file that the precise atom identities can be found. You can infer them from the PDB lines, but that rather misses the point. Frank On 19/05/2023 10:42, Fred Vellieux wrote: Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://datascience.unm.edu/tomcat/biocomp/convert Sometimes the conversion doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my collaborator couldn't find them. Any pointers welcome. (To save us time.) Thanks! Frank 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] how to get mol files from PDB and restraint CIF?
Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://datascience.unm.edu/tomcat/biocomp/convert Sometimes the conversion doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my collaborator couldn't find them. Any pointers welcome. (To save us time.) Thanks! Frank 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/ -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic 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] how to get mol files from PDB and restraint CIF?
Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my collaborator couldn't find them. Any pointers welcome. (To save us time.) Thanks! Frank 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/
