Re: [ccp4bb] mmciif pdb file editor.
PDBj has a nice web-based mmCIF editor that can help you edit mmCIF an validate the data entered. See https://pdbj.org/cif-editor/ Regards, Mitch Quoting Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>: Hi There is no particular special editor from PDB (or from anywhere else, as far as I know) for doing this - mmCIF is basically a simple text file with a defined set of contents. It frees you from the tyranny of fixed-width columns that your have in the historic PDB file. I’d just use whatever text editor you have on your system - so on LInux or Mac, something like vim, emacs, nano, on Windows Notepad. No need for anything special. But I’d also be wary about screwing up the file completely with your edits - it’s easy to turn a compliant file into something invalid. Harry On 30 Aug 2023, at 14:05, Krishnan Raman wrote: How do I edit mmcif files from pdb? Is there a editor for download from pdb website? Thanks krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!BuQPrrmRaQ!izeB4_rSNqs9Q3BOWYMC8mBdT_ICR-FLWa5oRekUKzB50YixLm3GFzFFjlhA9lebGr_tRjUQ3xtJDXJXQ7kO45MANjNNN6VQpaiShgQImPI$ To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!BuQPrrmRaQ!izeB4_rSNqs9Q3BOWYMC8mBdT_ICR-FLWa5oRekUKzB50YixLm3GFzFFjlhA9lebGr_tRjUQ3xtJDXJXQ7kO45MANjNNN6VQpaiShgQImPI$ This message was issued to members of https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!BuQPrrmRaQ!izeB4_rSNqs9Q3BOWYMC8mBdT_ICR-FLWa5oRekUKzB50YixLm3GFzFFjlhA9lebGr_tRjUQ3xtJDXJXQ7kO45MANjNNN6VQpaiSSBM6vaY$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!BuQPrrmRaQ!izeB4_rSNqs9Q3BOWYMC8mBdT_ICR-FLWa5oRekUKzB50YixLm3GFzFFjlhA9lebGr_tRjUQ3xtJDXJXQ7kO45MANjNNN6VQpaiS6WNKbt4$ , terms & conditions are available at https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!BuQPrrmRaQ!izeB4_rSNqs9Q3BOWYMC8mBdT_ICR-FLWa5oRekUKzB50YixLm3GFzFFjlhA9lebGr_tRjUQ3xtJDXJXQ7kO45MANjNNN6VQpaiSTQn5kNg$ 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] mmciif pdb file editor.
https://pdbj.org/cif-editor/ HTH, Luca From: CCP4 bulletin board on behalf of Krishnan Raman Reply to: Krishnan Raman Date: Wednesday, 30 August 2023 at 15:06 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] mmciif pdb file editor. You don't often get email from rkrish...@biocryst.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> How do I edit mmcif files from pdb? Is there a editor for download from pdb website? Thanks krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. 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] mmciif pdb file editor.
Dear Krish, As Harry mentioned, a simple text editor will work. May I recommend using Visual Studio Code using the CIF extension by Heikki Kainulainen? https://github.com/hmkainul/vscode-cif / https://marketplace.visualstudio.com/items?itemName=thisperiodictable.cif Cheers, Deborah On 31/08/2023 09:06, Harry Powell wrote: Hi There is no particular special editor from PDB (or from anywhere else, as far as I know) for doing this - mmCIF is basically a simple text file with a defined set of contents. It frees you from the tyranny of fixed-width columns that your have in the historic PDB file. I’d just use whatever text editor you have on your system - so on LInux or Mac, something like vim, emacs, nano, on Windows Notepad. No need for anything special. But I’d also be wary about screwing up the file completely with your edits - it’s easy to turn a compliant file into something invalid. Harry On 30 Aug 2023, at 14:05, Krishnan Raman wrote: How do I edit mmcif files from pdb? Is there a editor for download from pdb website? Thanks krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. 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/ -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK http://www.PDBe.org --- 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] mmciif pdb file editor.
Hi There is no particular special editor from PDB (or from anywhere else, as far as I know) for doing this - mmCIF is basically a simple text file with a defined set of contents. It frees you from the tyranny of fixed-width columns that your have in the historic PDB file. I’d just use whatever text editor you have on your system - so on LInux or Mac, something like vim, emacs, nano, on Windows Notepad. No need for anything special. But I’d also be wary about screwing up the file completely with your edits - it’s easy to turn a compliant file into something invalid. Harry > On 30 Aug 2023, at 14:05, Krishnan Raman wrote: > > How do I edit mmcif files from pdb? Is there a editor for download from pdb > website? Thanks krish > > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally > privileged information that is intended only for the individual or entity to > whom it is addressed. If you are not the intended recipient, please be > advised that any dissemination, distribution or copying of this email and any > attachment is strictly prohibited. If you have received this email in error, > please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take > corrective measures and then permanently delete this email and any > attachment, including any printed copies. Thank you. > > > 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/
[ccp4bb] mmciif pdb file editor.
How do I edit mmcif files from pdb? Is there a editor for download from pdb website? Thanks krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. 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/
