Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query
> It sounds as though you need the power of the script. You can (from memory) > run pdbcur to drop the aniso lines and hydrogen atoms, which helps. Or from command-line: gemmi convert --anisou=no --remove-h in.pdb out.pdb > You could probably get it to delete everything except CA's too. this would be: gemmi convert --select='CA[C]' --anisou=no --minimal in.pdb out.pdb (--minimal drops REMARKs and other metadata) 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] AW: [ccp4bb] a dinosaur asks ... PDB format query
Dear Jon, If I understand your question right, I would use Gemmi for this purpose: https://gemmi.readthedocs.io/en/latest/mol.html https://gemmi.readthedocs.io/en/latest/analysis.html It's not in GUI, it involves scripting in Python. It's a very powerful tool and capable of working with both PDB and mmCIF formats and with both proteins and nucleic acids. Cheers, Martin On 15/05/2024 13:11, Hughes, Jonathan wrote: hello CCP4 people, rather off-topic: is there a purpose-written windows editor for PDF files? with interleaved anisotropy lines, missing column delimiters etc., simply extracting the B-factors for Ca atoms is hard work using a standard character editor. would anyone think of working with DNA without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics Free University of Berlin & Institute for Plant Physiology Justus Liebig University Giessen Germany 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] AW: [ccp4bb] a dinosaur asks ... PDB format query
You could probably get it to delete everything except CA's too. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 15 May 2024, 13:22, Jon Cooper wrote: > It sounds as though you need the power of the script. You can (from memory) > run pdbcur to drop the aniso lines and hydrogen atoms, which helps. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > Sent from Proton Mail mobile > > Original Message > On 15 May 2024, 13:11, Hughes, Jonathan wrote: > >> hello CCP4 people, rather off-topic: is there a purpose-written windows >> editor for PDF files? with interleaved anisotropy lines, missing column >> delimiters etc., simply extracting the B-factors for Ca atoms is hard work >> using a standard character editor. would anyone think of working with DNA >> without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics >> Free University of Berlin & Institute for Plant Physiology Justus Liebig >> University Giessen Germany >> 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 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] AW: [ccp4bb] a dinosaur asks ... PDB format query
It sounds as though you need the power of the script. You can (from memory) run pdbcur to drop the aniso lines and hydrogen atoms, which helps. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 15 May 2024, 13:11, Hughes, Jonathan wrote: > hello CCP4 people, rather off-topic: is there a purpose-written windows > editor for PDF files? with interleaved anisotropy lines, missing column > delimiters etc., simply extracting the B-factors for Ca atoms is hard work > using a standard character editor. would anyone think of working with DNA > without proper tools? best jon -- Prof. Dr. Jon Hughes Department of Physics > Free University of Berlin & Institute for Plant Physiology Justus Liebig > University Giessen Germany > 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/
