Re: [ccp4bb] PDB validation - oligosacchides
Hi Natalie, comp_id needs to be a valid CCD ID, in this case 'GLC'. Not sure why/how the invalid value 'GLC-b-D' was generated. Let us know if you need further assistance, Deborah On 03/05/2024 22:25, Natalie Losada wrote: I am validating a structure with two sucrose molecules. I am getting the following error when uploading the file: ERROR: In 'data_comp_GLC' block: In 'chem_comp_atom' category: The 'comp_id' field value 'GLC-b-D' is not same as 'GLC' defined in data block name. I have copied sucrose directly from 5d3g.cif in Coot, and refined in phenix. I have also made the sucrose manually and acquired the cif from another website, followed by placement in Coot and refinement with phenix. Any thoughts how to save the file in a way that PDB will accept? Natalie 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/
[ccp4bb] Coming soon: Annotation of Protein Modifications in the PDB
Dear all, The standardization of protein modification handling ensures that there is a single correct approach to handling each protein modification that occurs within the PDB archive. However, there are many existing PDB entries that contain protein modifications which do not follow these handling conventions. As part of the protein modifications remediation project, all model coordinates files containing protein modifications are being re-released to add a new protein modification data category. This new category will list all observed PCMs/PTMs within the entry, as well as their type and category, allowing better findability. A new category will also be added to the Chemical Component Definition (CCD) files. It will state whether the CCD is a known PCM, its type and category, as well as on which positions in the amino acid and in the polypeptide it is expected to be observed. If this PCM is also a known PTM, it will have the Uniprot generic PTM accession ID. Finally, any protein modifications that are inconsistently handled within a PDB entry will be amended, to ensure that a given modification is consistently handled in the PDB archive. Detailed information about this work is available from GitHub, including PDBx/mmCIF dictionary extension and a set of example files, and complete documentation of the additional annotation: https://github.com/wwPDB/protein-modification-extension Questions or feedback? Contact deposit-h...@mail.wwpdb.org. The protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project is a wwPDB collaborative project carried out principally by PDBe at EMBL-EBI, and is funded by BBSRC grant number BB/V018779/1. Read this news online <https://www.wwpdb.org/news/news?year=2024#662fa1a565d8a8cacaf76f9c> Kind regards, Deborah Harrus, on behalf of the wwPDB -- --- 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] add ligand with AceDRG
Thanks for the feedback, I will let PDBe developers know that this is causing confusion and that LIG should not return results. Kind regards, Deborah On 26/04/2024 16:11, Garib Murshudov wrote: On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligand. With small letters it says: The chemical component you are trying to view (LIG) has been obsoleted. You have been redirected to the component which superceded it. On RCSB website it does not return anything. Perhaps, on the PDBe website it could also not return anything. Regards Garib On 26 Apr 2024, at 16:07, Deborah Harrus wrote: Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote: Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent from my iPhone On Apr 25, 2024, at 8:03 AM, Nicholas Clark <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: EXTERNAL MAIL Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice. Obviously, just make sure your existing selection does not exist in the PDB. Best, Nick Clark On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson wrote: Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE wrote: Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with existing library entries. Is there any way around this? How do I add a novel ligand? Thanks so much for your help. Best wishes, Stefanie Dr. Stefanie Freitag-Pohl (she/her) Durham University Department of Chemistry South Road, Durham DH1 3LE United Kingdom 0191 334 2596 stefanie.freitag-p...@durham.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$> Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com <https://urldefense.com/v3/__http://www.saromics.com__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6Sf4INmI8$> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C
Re: [ccp4bb] add ligand with AceDRG
Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote: Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent from my iPhone On Apr 25, 2024, at 8:03 AM, Nicholas Clark <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: EXTERNAL MAIL Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice. Obviously, just make sure your existing selection does not exist in the PDB. Best, Nick Clark On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson wrote: Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE wrote: Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with existing library entries. Is there any way around this? How do I add a novel ligand? Thanks so much for your help. Best wishes, Stefanie Dr. Stefanie Freitag-Pohl (she/her) Durham University Department of Chemistry South Road, Durham DH1 3LE United Kingdom 0191 334 2596 stefanie.freitag-p...@durham.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$> Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com <https://urldefense.com/v3/__http://www.saromics.com__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6Sf4INmI8$> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$> -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 To unsubscribe from
Re: [ccp4bb] add ligand with AceDRG
Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent from my iPhone On Apr 25, 2024, at 8:03 AM, Nicholas Clark <b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: EXTERNAL MAIL Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice. Obviously, just make sure your existing selection does not exist in the PDB. Best, Nick Clark On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson wrote: Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE wrote: Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with existing library entries. Is there any way around this? How do I add a novel ligand? Thanks so much for your help. Best wishes, Stefanie Dr. Stefanie Freitag-Pohl (she/her) Durham University Department of Chemistry South Road, Durham DH1 3LE United Kingdom 0191 334 2596 stefanie.freitag-p...@durham.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$> Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com <https://urldefense.com/v3/__http://www.saromics.com__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6Sf4INmI8$> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$> -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6SdhSxg4M$> CAUTION: This email originated from
Re: [ccp4bb] Rescale merged data?
Dear all, Just to reiterate that wwPDB can accept multiple data blocks of data before and after process, and the first block should be the one that used for the refinement of the deposited coordinates. Kind regards, Deborah On 18/04/2024 13:37, Randy John Read wrote: I haven’t deposited any PDB entries for a while. The last time I did, I remember it not being completely trivial to add these loops. However, I was hoping that someone from wwPDB or CCP4 would weigh in with advice on how it can be done! For those who use StarAniso, the current version makes a CIF file with the required loops, and they now have advice on their website about this: https://staraniso.globalphasing.org/deposition_about.html. Randy -- --- 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/
[ccp4bb] wwPDB News: NMR Restraint Validation Paper Published
Dear all, We are pleased to announce the publication of this manuscript, addressing the challenge of validation of experimental biomolecular NMR structures against restraint data. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data harvesting system. The resulting wwPDB Restraint Violation Report provides a model vs data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints. We present the rationale for model-vs-data restraint validation by the wwPDB, together with summary of validation tools and reports for NMR distance and dihedral restraints that have been developed, as implemented in the wwPDB validation pipeline and recommended by the wwPDB NMR-VTF committee. *Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank* Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, Yuhe Liang, Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin Bardiaux, Charles Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, Gaetano T Montelione, Geerten W Vuister, Jasmine Y Young (2024)/Structure/32, 1–14: doi:10.1016/j.str.2024.02.011 <https://doi.org/10.1016/j.str.2024.02.011> The wwPDB plans to further enhance validation report by providing model-vs-data quality assessment for other kinds of restraints based on community recommendation and improve data representation on structures with multiple conformation states. Kind regards, Deborah Harrus, on behalf of the wwPDB -- --- 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/
[ccp4bb] New, free online AlphaFold training course
Dear all, Recognising the transformative impact of AlphaFold on scientific research, EMBL-EBI and Google DeepMind have co-developed a comprehensive online training course to facilitate the wider adoption and responsible use of this technology. The training course, launched last week offers an interactive learning experience tailored to different levels of expertise. It enables users to delve into the fundamentals of AlphaFold, explore its strengths and limitations, and gain practical skills through hands-on exercises. The AlphaFold training course is now available on the EMBL-EBI Training platform: https://www.ebi.ac.uk/training/online/courses/alphafold/ If you have any questions about the course, please reach out to the EMBL-EBI training team on trainonl...@ebi.ac.uk. Kind regards, Deborah Harrus PDBe -- --- 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/
[ccp4bb] wwPDB News: CryoEM Archiving and Validation Recommendations
Dear all, A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and setting community recommendations. The outcomes of this meeting have now been published in this manuscript which highlights the recent achievements made by the wwPDB in the space of 3DEM validation and the community recommendations going forward. Some of these recommendations have already been implemented, such as a three-tiered strategy powered by the Validation Analysis (VA) pipeline for the dissemination of validation information and ensuring the that VA can be run by external applications. *Community recommendations on cryoEM data archiving and validation* Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H.W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar (2024)/IUCrJ/11: 140–151https://doi.org/10.1107/S2052252524001246 Kind regards, Deborah Harrus on behalf of the wwPDB -- --- 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/
[ccp4bb] wwPDB News: Latest Developments on the EMDB Published
Dear all, We are please to announce the publication of this manuscript, addressing the recent developments in the archiving of 3DEM data and the future plans for the EMDB. The burgeoning popularity of the electron microscopy field has been coupled with new technologies and software solutions, together this has pushed exponential growth in yearly depositions, increases in the resolution of the deposited data, and, consequently, accuracy of molecule models associated with 3DEM data. As the EMDB continues to grow it remains dedicated to delivering a world-class archive that adheres to FAIR principles. In addition, we recognise the importance of easy and open access to accurately curated data for the various users of the archive, we plan to continue to facilitate and enhance this moving forward. EMDB—the Electron Microscopy Data Bank The wwPDB Consortium Nucleic Acids Research (2024) 52: D456–D465 https://doi.org/10.1093/nar/gkad1019 Kind regards, Deborah Harrus on behalf of the wwPDB -- --- 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] Crystallizing a tough target
Dear Kavya, I'm sure there are several similar stories to learn from. I've worked with a point-mutant of a "normal" protein which made it thermostable - as revealed by DSF. It also resulted in an increased solubility, and the thing could be concentrated to 100 mg/mL and left on the bench for weeks with no alteration. It crystallized, but sadly (and understandably) never diffracted. One option for crystallizing your protein could be to look for buffers which make it a bit less soluble? So you wouldn't have to concentrate it to so high values, and start nucleation at a lower concentration? Again, scanning several buffers/protein concentration ratios, using DSF, would be one possibility. You're looking for the sweet spot to start nucleation. Don't be afraid to try uncommon buffers, pH values, temperatures. Other option would be to test using nucleanting agent - crystallophores, Naomi's nucleant, nanodiamonds, dried seaweed powder, hair... Or even a crystal seed from another protein might help. Good luck! Deborah On 05/02/2024 10:27, kavyashreem wrote: Dear All, Has anyone worked on a protein which is highly soluble even at 80mg/ml? We have one such candidate, which does not precipitate even at 80mg/ml instead forms phase separated globules in crystallization plate, which eventually hardens over a period of 1 to 1.5 months (which is florescent under UV microscope.) We tried screening at different pH, but failed to get any hits. Since we got few conditions in which the phase separated globules solidified, we focused on them and expanded with 120mg/ml protein, still there were not visible precipitates except for the phase separation. This has been a challenging target so far. We have tried with different constructs, which unfortunately are not soluble! Does POMs help in such cases? Or do you have any other suggestion. Thank you Regards Kavya *CONFIDENTIAL: This email and any files transmitted with it are confidential and intended solely for the use of the individual or group to whom they are addressed. If you have received this email in error, please notify the sender immediately and delete this e-mail from your system. It is NOT AUTHORISED to copy, forward, or in any way reveal the contents of this message to anyone.* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- ------- 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] Error in "Prepare and validate files for deposition" task"
Dear Maria, Apologies for late reply. I'm not sure which version of "adding_stats_to_mmcif" is in CCP4 at the moment, but if you're facing the issue again in the future please could you try using the latest version at https://github.com/wwPDB/py-adding_stats_to_mmcif ? If it doesn't work, please feel free to send me your file and I will troubleshoot. Kind regards, Deborah Harrus PDBe On 30/01/2024 17:36, mdimarog wrote: Dear all, I am trying to deposit 2 structures to the PDBe, solved and refined in CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars in. To this end, I used "Prepare and validate files for deposition" task, as I had previously (and succesfully) done. However, and in spite of switching to the latest CCP4 version (8.0.017), I keep getting this error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to add 204". I am using macOS Monterey, version 12.6.5. Does anybody have an idea what is going wrong? If not, does anybody know a different way to submit the reflection data to the PDBe? For example, would this be somehow possible just using the output from Refmac and AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure because there are a lot of sugars there, quite difficult to built. Many thanks in advance for your help! Kind regards, Maria -- ----------- 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] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files
Dear Frank, We are indeed harvesting restraints used in refinement, but not distributing them yet. This should come later this year or early 2025, and can be made retrospectively. Kind regards, Deborah On 31/01/2024 14:15, Frank von Delft wrote: Hi Deborah - sounds great, well done! Are you yet harvesting and serving up the restraints used in refinement? If not, that remains a huge gap, in my view. (The chemists tend not to be aware that's even a thing, I keep discovering.) Frank On 31/01/2024 13:57, Deborah Harrus wrote: *Dear all,* *We're excited to announce significant improvements to ligand data access and organisation within the PDBe FTP area. These updates aim to empower your research by simplifying data retrieval and providing deeper insights into protein-ligand interactions.* *Key Enhancements:* * *Comprehensive Ligand Interaction Data: Two new data files, Interacting_chains_with_ligand_functions.tsv and pdb_bound_molecules.tsv, enable large-scale analyses of ligand interactions across the entire PDB archive including functional categorisation such as drug-like, reactant-like or cofactor-like.* * *Streamlined FTP Directory Structure: The revamped FTP area features dedicated folders for Chemical Component Definitions (CCDs), Peptide-like Reference Definitions (PRDs), Covalently Linked Components (CLCs), and additional data files, facilitating intuitive data navigation.* *Benefits for You:* * *Perform large-scale ligand interaction analyses across the entire PDB using complete ligand representations.* * *Quick access to all the ligands bound to a specific protein or identifying all the proteins binding to a specific ligand* * *Gain deeper insights into protein function through ligand interaction and classification.* * *Easily access and navigate ligand data with clear file organisation and unique identifiers.* *We believe these improvements will enhance ligand data analysis through streamlined data access and additional functional insights. * *For more information, visit the PDBe news item at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp <https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp>* *Or visit the PDBe FTP area directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ <https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/>* *Should you have any questions or require further assistance, please don't hesitate to contact us.* * Sincerely, Deborah Harrus The PDBe Team * -- ------- 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 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- ----------- 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/
[ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files
** *Dear all,* *We're excited to announce significant improvements to ligand data access and organisation within the PDBe FTP area. These updates aim to empower your research by simplifying data retrieval and providing deeper insights into protein-ligand interactions.* *Key Enhancements:* * *Comprehensive Ligand Interaction Data: Two new data files, Interacting_chains_with_ligand_functions.tsv and pdb_bound_molecules.tsv, enable large-scale analyses of ligand interactions across the entire PDB archive including functional categorisation such as drug-like, reactant-like or cofactor-like.* * *Streamlined FTP Directory Structure: The revamped FTP area features dedicated folders for Chemical Component Definitions (CCDs), Peptide-like Reference Definitions (PRDs), Covalently Linked Components (CLCs), and additional data files, facilitating intuitive data navigation.* *Benefits for You:* * *Perform large-scale ligand interaction analyses across the entire PDB using complete ligand representations.* * *Quick access to all the ligands bound to a specific protein or identifying all the proteins binding to a specific ligand* * *Gain deeper insights into protein function through ligand interaction and classification.* * *Easily access and navigate ligand data with clear file organisation and unique identifiers.* *We believe these improvements will enhance ligand data analysis through streamlined data access and additional functional insights. * *For more information, visit the PDBe news item at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp <https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp>* *Or visit the PDBe FTP area directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ <https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/>* *Should you have any questions or require further assistance, please don't hesitate to contact us.* * Sincerely, Deborah Harrus The PDBe Team * -- ------- 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/
[ccp4bb] wwPDB Preprint Published on NextGen Archive
Dear all, A new paper describes how therecently-announced NextGen Archive <https://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826>provides centralized access to integrated annotations and enriched structural information for PDB data: *NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank* Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley (2023)/bioRxiv/doi:10.1101/2023.10.24.563739 <https://doi.org/10.1101/2023.10.24.563739> ThePDB NextGen archive <https://www.wwpdb.org/ftp/pdb-nextgen-archive-site>provides sequence annotation from external resources such as UniProt, SCOP2 and Pfam in addition to the content provided in the structure model files in the PDB main archive. The inclusion of UniProtKB numbering facilitates effortless structural comparisons between experimental and predicted protein models. These PDBx/mmCIF files are directly compatible with various data visualization tools, simplifying the display of annotations on 3D structure views. Read this news online: https://www.wwpdb.org/news/news?year=2024#65b3f0e0c76ca3abcc925d12 Kind regards, Deborah Harrus, on behalf of the wwPDB -- ----------- 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/
[ccp4bb] wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)
Dear all, wwPDB anticipates that all the four character PDB accession codes (PDB ID) will be consumed by 2029. With the continuous growth of PDB archive, wwPDB has revised the PDB accession code format by extending its length and prepending “PDB” (e.g., "1abc" will become "pdb_1abc"). This process will enable text mining detection of PDB entries in the published literature and allow for more informative and transparent delivery of revised data files. Entries with extended PDB IDs (12 characters) will not be compatible with the legacy PDB file format once four-character PDB IDs are consumed. wwPDB encourages scientific journals, PDB community and users to transition to using the PDBx/mmCIF format and the extended PDB ID format as soon as possible. Resources are available to help PDB users with this transition through thewwPDB resource portal page (Extended PDB ID With 12 Characters) <https://www.wwpdb.org/documentation/new-format-for-pdb-ids>. This page links to useful resources for handling this change, including anFAQ on PDB ID extension <https://www.wwpdb.org/documentation/pdb-id-extension-faq>, materials to learn more about PDBx/mmCIF format, and links to other PDBx/mmCIF resources and software tools. As the transition phase progresses, more training resources will be added to this page. Additionally, a PDB “beta” archive will be provided during the transition phase in 2026. The directory structure of this “beta” archive will mirror the data organization of thePDB Versioned Archive <http://files-versioned.wwpdb.org/>in the form of https://files-beta.org/pub/pdb/data/entries//two-letter-hash///pdb_accession_code///entry_data_File_names/. The two-letter hash will be based on the n-2 and n-3 characters. For example, PDB entry PDB_12345678 will be under /67/. This will maintain consistency with the current PDB archive, where e.g. PDB entry 1abc is under /ab. Once all the four character PDB accession codes are consumed, this PDB “beta” archive will become the PDB main archive and the current PDB archive will be removed. Download example files containing extended PDB IDs for software adoptionfrom GitHub <https://github.com/wwPDB/extended-wwPDB-identifier-examples>. wwPDB recently announced that PDB three-character Chemical Component IDs have been consumed. <https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6>Five-character alphanumeric accession codes for CCD IDs are now issued by the OneDep system. For any further information please contact us ati...@wwpdb.org. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ----------- 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/
[ccp4bb] wwPDB News: Time-stamped Copies of PDB and EMDB Archives
Dear all, A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org,https://s3.rcsb.org) as of January 2, 2024 has been added toftp://snapshots.wwpdb.org,https://s3snapshots.rcsb.org(AWS), andftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive. The directory 20240101 includes the 214,121 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 1,242 GB. A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 01, 2024 can be found inftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20240101/andftp://snapshots.pdbj.org/20240101/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (32,033 and 282, respectively) and is 14 TB in size. Read this news online <https://www.wwpdb.org/news/news?year=2024#65959344d78e004e766a96cf> Kind regards, Deborah Harrus, on the behalf of wwPDB -- --- 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] "LINK" and "REMARK 290" of pdb file
Dear Qixu, You can take a look at existing entries which have link records between 1_555 and another symmetry molecule. For example 5BQC which has various of these. mmCIF: # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ?? A CYS 7 SG ? ? ? 1_555 A CYS 68 SG ? ? B CYS 45 B CYS 106 1_555 ? ? ? ? ? ? ? 2.032 ?? disulf2 disulf ?? A CYS 15 SG ? ? ? 1_555 A CYS 61 SG ? ? B CYS 53 B CYS 99 1_555 ? ? ? ? ? ? ? 2.031 ?? disulf3 disulf ?? A CYS 52 SG ? ? ? 1_555 A CYS 90 SG ? ? B CYS 90 B CYS 128 1_555 ? ? ? ? ? ? ? 2.027 ?? disulf4 disulf ?? A CYS 79 SG ? ? ? 1_555 A CYS 120 SG ? ? B CYS 117 B CYS 158 1_555 ? ? ? ? ? ? ? 2.030 ?? disulf5 disulf ?? A CYS 83 SG ? ? ? 1_555 A CYS 107 SG ? ? B CYS 121 B CYS 145 1_555 ? ? ? ? ? ? ? 2.031 ?? disulf6 disulf ?? B CYS 18 SG ? ? ? 1_555 B CYS 75 SG ? ? A CYS 39 A CYS 96 1_555 ? ? ? ? ? ? ? 2.009 ?? disulf7 disulf ?? B CYS 34 SG ? ? ? 1_555 B CYS 89 SG ? ? A CYS 55 A CYS 110 1_555 ? ? ? ? ? ? ? 2.029 ?? disulf8 disulf ?? B CYS 44 SG ? ? ? 1_555 B CYS 105 SG ? ? A CYS 65 A CYS 126 1_555 ? ? ? ? ? ? ? 2.039 ?? disulf9 disulf ?? B CYS 48 SG ? ? ? 1_555 B CYS 107 SG ? ? A CYS 69 A CYS 128 1_555 ? ? ? ? ? ? ? 2.010 ?? disulf10 disulf ?? B CYS 72 SG ? ? ? 1_555 B CYS 74 SG ? ? A CYS 93 A CYS 95 7_555 ? ? ? ? ? ? ? 1.996 ?? covale1 covale one ? A ASN 21 ND2 ? ? ? 1_555 E NAG . C1 ? ? B ASN 59 B NAG 202 1_555 ? ? ? ? ? ? ? 1.446 ? N-Glycosylation covale2 covale one ? A ASN 106 ND2 ? ? ? 1_555 D NAG . C1 ? ? B ASN 144 B NAG 201 1_555 ? ? ? ? ? ? ? 1.440 ? N-Glycosylation covale3 covale none ? A HIS 116 NE2 ? ? ? 1_555 C GU4 . O29 ? ? B HIS 154 C GU4 1 10_444 ? ? ? ? ? ? ? 1.458 ?? covale4 covale none ? B ARG 86 NH1 ? ? ? 1_555 C YYJ . C6 ? ? A ARG 107 C YYJ 2 10_444 ? ? ? ? ? ? ? 1.287 ?? covale5 covale both ? C GU4 . C1 ? ? ? 1_555 C YYJ . O2 ? ? C GU4 1 C YYJ 2 1_555 ? ? ? ? ? ? ? 1.370 sing ? # PDB: LINK ND2 ASN B 59 C1 NAG B 202 1555 1555 1.45 LINK ND2 ASN B 144 C1 NAG B 201 1555 1555 1.44 LINK NE2 HIS B 154 O29 GU4 C 1 1555 10444 1.46 LINK NH1 ARG A 107 C6 YYJ C 2 1555 10444 1.29 LINK C1 GU4 C 1 O2 YYJ C 2 1555 1555 1.37 Let me know if you need further assistance. Kind regards, Deborah Harrus PDBe On 29/12/2023 12:12, Qixu Cai wrote: Dear all, I'm working on the refinement of a crystal structure. In the structure, one crystal packing interface is mediated by a compound with two coordinate covalent bonds to two macromolecules from different asymmetric units. Thus I need to specify two "LINK" records in the head of pdb file. The "LINK" record between the compound and macromolecule in the same asymmetric unit is generated by refmac automatically. However, refmac does not generate the other "LINK" between the compound and the symmetric macromolecule. Thus I want to add the LINK record myself. As the LINK is between different symmetric molecules, I need to specify the symmetry code, such as "1555", "2555" and so on. The symmetry code is dependent on the "REMARK 290" record. My question is: 1. How can I generate the "REMARK 290" information? 2. Any easier method to generate the "LINK" record between molecules from different asymmetric units? Thanks a lot for your help! Best regards, Qixu Cai Email: caiq...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?
[ccp4bb] wwPDB News: Improved Depositor Experience Using ORCiD
Dear all, SinceMarch 2023 <https://www.wwpdb.org/news/news?year=2023#641872ffe0a2cc03bf315460>, depositors can use their ORCiDs to access the OneDep system. This authentication method enables contact authors to access sessions without sharing passwords. Using ORCiD with OneDep returns a summary table of all entries in which the ORCiD has been provided for the contact author. We have improved the summary table with: * Two new columns display the experimental method and the hold expiration date * EMDB and BMRB accession codes for EM and NMR displayed alongside the entry ID * All columns now sortable While using a deposition ID and password to login into OneDep is still possible, we encourage depositors to use ORCiD for an improved user experience. Questions or feedback? contactdeposit-h...@mail.wwpdb.org. Kind regards, Deborah Harrus, on behalf of the wwPDB -- --- 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/
[ccp4bb] wwPDB News - PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats
Dear all, The PDB three-character Chemical Component IDs are consumed and *PDB has begun issuing five-character alphanumeric accession codes for CCD IDs in the OneDep system*. To avoid confusion with current four-character PDB IDs, four-character codes are not used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes are distributed in PDBx/mmCIF and PDBML formats and will not be supported by the legacy PDB file format (see previous announcement <https://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7>). In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB. These reserved codes can be used for new ligands during structure determination so that they can be identified as new upon deposition and added to the CCD during biocuration. wwPDB is asking users and software developers to review their code and remove any current limitations on PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended PDB and/or CCD IDs are available via GitHub <https://github.com/wwPDB/extended-wwPDB-identifier-examples>to assist with code revisions. To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/ <https://www.wwpdb.org/news/mmcif.wwpdb.org/>. For any further information please contact us at i...@wwpdb.org Kind regards, Deborah Harrus, on behalf of the wwPDB -- ----------- 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/
[ccp4bb] wwPDB News: Backbone Annotation and Standardization of Peptide Residues is Now Live
Dear all, The wwPDB has rolled out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs have been updated accordingly. This improves the Findability and Interoperability of the PDB data and opens up new opportunities to use the updated peptide residue annotation. As announced previously <https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687>, new data items have been added to the CCD files for peptide-linking components to label atoms that form the backbone, N- or C-terminal groups. Three new CCD data items have been added to the CCD category _chem_comp_atom as pdbx_backbone_flag, pdbx_N-terminal_flag and pdbx_C-terminal_flag, flagging the backbone, N-terminal and C-terminal atoms, respectively. Furthermore, we have standardized the atom nomenclature of peptide backbone atoms in CCD files to follow a standard convention. This follows a set of rules, outlined in ourdocumentation <https://www.wwpdb.org/documentation/peptides-remediation>, ensuring that atom nomenclature for carboxyl groups, amino groups and side chain linked carbons (C-alpha) follow a standard atom nomenclature. This allows clear identification of backbone atoms for peptide residues across the whole archive. Questions or feedback? contactdeposit-h...@mail.wwpdb.org. The peptide residues chemical component dictionary remediation project is part of the protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project, a wwPDB collaborative project carried out principally byPDBe <https://www.ebi.ac.uk/pdbe/>atEMBL-EBI <https://www.ebi.ac.uk/>, and is funded by BBSRC grant number BB/V018779/1. Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- 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/
[ccp4bb] AlphaFold Database introduces sequence-based search and structure cluster members
Dear all, We are excited to announce two significant functionalities added to the AlphaFold Protein Structure Database (AlphaFold DB). The database has expanded since its inception in 2021 to cover over 214 million predicted structures from Google Deepmind’s AlphaFold 2 system. We now introduce sequence similarity-based search and enhanced prediction pages by displaying structurally similar predictions. The sequence-similarity search is powered by the Basic Local Alignment Search Tool (BLAST <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata>) which enables finding relevant predicted structures based on a protein sequence. Sequence search results have been integrated to our current search results pages, highlighting reviewed status and reference proteome. In a collaboration with the Steinegger lab and to make the navigation of the structural landscape easier, we have incorporated the clustering algorithm, Foldseek Cluster <https://www.nature.com/articles/s41586-023-06510-w>. For a streamlined experience, we have added the new structure similarity cluster feature that has been added directly to the prediction pages. We believe that these new features will make AlphaFold DB even more useful and accessible to the scientific community. To learn more, please visit the AlphaFold DB website at https://alphafold.ebi.ac.uk/. For more information about the new features, visit: https://www.ebi.ac.uk/about/news/updates-from-data-resources/alphafold-database-update-sequence-based-search/ Kind regards, Deborah Harrus PDBe -- ------- 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/
[ccp4bb] PDBe ligands API survey - please give us your feedback
Dear all, We are excited to inform you of some upcoming enhancements to PDBe's ligand-related API endpoints and are seeking your valuable insights! *We are running this survey (https://forms.gle/agPUGCn59ffuayp57) *to collect information on two crucial points: - *Current Usage of PDBe's Ligand-Related API Endpoints*: We want to understand which of PDBe's existing ligand-related API functionalities you currently use, if any. - *Requirements for Future API Endpoints*: We are interested in any additional functionalities or features you want to see to enhance your workflows Completing this survey should take approximately 10 minutes of your time. *Survey Deadline: October 24th.* Your participation is greatly appreciated, and we look forward to creating an even better PDBe experience together. Thank you for your time and consideration. Kind regards, Deborah Harrus -- --- 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/
[ccp4bb] wwPDB News: Distribution of Electron Microscopy metadata in PDBx/mmCIF file format
Dear all, At the beginning of October 2023, the Electron Microscopy Data Bank (EMDB) will start distributing electron microscopy (EM) metadata for its entries in PDBx/mmCIF file format alongside the already available XML formatted files. The addition of PDBx/mmCIF files in the archive will bring parity between EMDB and PDB (EM experimental data vs 3D structures) in the way metadata is served while improving the consistency and interoperability between the two archives. EMDB entries released before October 2023 will have PDBx/mmCIF files added at a later date. The description of PDBx/mmCIF categories and items featured in EM metadata files can be found in the PDBx/mmCIF dictionary <https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html>. For an EMDB entry EMD-x, PDBx/mmCIF file name will be emd-x.cif.gz and it will be located in the entry's subfolder called metadata (EMD-x/metadata) in the wwPDB archive repositories: * EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/structures/ * wwPDB: https://files.wwpdb.org/pub/emdb/structures/ * RCSB PDB (US): https://files.rcsb.org/pub/emdb/structures/ * PDBe (UK): https://ftp.ebi.ac.uk/pub/databases/emdb/structures/ * PDBj (Japan): https://files.pdbj.org/pub/emdb/structures/ Read this news online <http://www.wwpdb.org/news/news?year=2023#651c49e2d78e004e766a96a4> Kind regards, Deborah Harrus, on behalf of the wwPDB -- ------- 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/
[ccp4bb] wwPDB NEWS: Announcing Kyle Morris as EMDB's New Team Leader
Dear all, wwPDB is excited to announce that Kyle Morris has joined the EMDB team as their new team leader. Kyle brings 10 years of experience in the cryo-EM field, and will draw on first-hand knowledge from his scientific research and staff roles within cryo-EM facilities. How the EMDB continues to engage with the community will be complemented with the experience Kyle gained developing and coordinating training programs during his time at eBIC. His vision for EMDB includes strengthening its core functions, developing connections to complementary databases, and preparing the archive for future cryo-EM technologies, including machine learning applications. Read this news online <https://www.wwpdb.org/news/news?year=2023#6513b759d78e004e766a96a3> Kind regards, Deborah Harrus, on behalf of wwPDB -- --- 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.
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/
[ccp4bb] Scientific Data Curator position (PDB and EMDB)
Dear all, We are looking to recruit an expert structural biologist or bioinformatician to join the PDBe curation team on the Wellcome Genome Campus near Cambridge. The work involves annotating preliminary PDB and EMDB submissions and extracting relevant biological information and will also involve analysis of structure data and enriching PDBe tools and services. The data curators also participate in developing training material and delivery of workshops and in outreach activities. The closing date for this post is 12th September 2023. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02149 Kind Regards Deborah Harrus -- --- 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/
[ccp4bb] wwPDB News: Updated Annotation and Standardization of Peptide Residues
Dear all, In October 2023, the wwPDB will roll out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs will also be updated accordingly. This will improve the Findability and Interoperability of the PDB data, as well as open up new opportunities to use the updated peptide residue annotation. As part of this remediation process, we will add new data items to the CCD files for peptide-linking components to label atoms that form the backbone, N- or C-terminal groups. Three new CCD data items will be added to the CCD category _chem_comp_atom as pdbx_backbone_flag, pdbx_n-terminal_flag and pdbx_c-terminal_flag, flagging the backbone, N-terminal and C-terminal atoms, respectively. Furthermore, we will be standardizing the atom nomenclature of peptide backbone atoms in CCD files to follow a standard convention. This will follow a set of rules, outlined in the documentation linked below, ensuring that atom nomenclature for carboxyl groups, amino groups and side chain linked carbons (C-alpha) follow a standard atom nomenclature. This will allow clear identification of backbone atoms for peptide residues across the whole archive. Detailed information about this work is available from the wwPDB website, including PDBx/mmCIF dictionary extension and example files (GitHub <https://github.com/wwPDB/backbone-extension>; Peptide Residues Chemical Component Dictionary Remediation Documentation <http://www.wwpdb.org/documentation/peptides-remediation>). Updated peptide CCDs will have standardized atom names and backbone / N- and C- terminal annotation./ / /Updated peptide CCDs will have standardized atom names and backbone / N- and C- terminal annotation./ We encourage developers of software packages for refinement or visualization of PDB data to review this information. Questions or feedback? Contact deposit-h...@mail.wwpdb.org. The peptide residues chemical component dictionary remediation project is part of the protein chemical modifications (PCMs) and post translational modifications (PTMs) remediation project, a wwPDB collaborative project carried out principally by PDBe at EMBL-EBI, and is funded by BBSRC grant number BB/V018779/1. Read this news online: https://www.wwpdb.org/news/news?year=2023#64bff95ed78e004e766a9687 Kind regards, Deborah Harrus -- ------- 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/
[ccp4bb] wwPDB News: PDB NextGen Archive Now Provides Intra-molecular Connectivity
Dear all, Version 1.0 of the next generation archive repository (NextGen) for the PDB archive was made available in early 2023 <http://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826>. This “NextGen” archive hosts enriched atomic coordinate files, in both PDBx/mmCIF and PDBML formats, with files available to download at files-nextgen.wwpdb.org <https://files-nextgen.wwpdb.org/>. The initial launch of the NextGen archive <http://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826> enriched coordinate files from the core PDB archive with sequence annotation from external resources such as UniProt, SCOP2 and Pfam at atom, residue, and chain levels. After consulting with user community, this release has added intra-molecular connectivity for each residue present in an entry, helping users transitioning from legacy PDB format to PDBx/mmCIF format <http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7>. The connectivity information includes atom pairs, bond order, aromatic flag, and stereochemistry as incorporated from the PDB Chemical Component Dictionary (CCD). Users can extract this information from the /_chem_comp_bond/ and /_chem_comp_atom/ categories of the PDBx/mmCIF-formatted files from the NextGen archive. To transition from legacy PDB format to PDBx/mmCIF, the file naming and data are structured based on extended PDB IDs <http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7> with a two letter hash code, ‘third from last character' and 'second from last character’. This hash code will remain consistent once PDB ID codes are extended beyond four characters with the pdb_ prefix, e.g., PDB entry 8aly: https://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_8aly/pdb_8aly_xyz-enrich.cif.gz. Users are encouraged to adopt PDBx/mmCIF format as early as possible. Learn more about PDBx/mmCIF format and related software resources at mmcif.wwpdb.org <https://mmcif.wwpdb.org/>. In the future, the PDB NextGen archive will continue to be updated with more enriched annotations from external database resources in the metadata, building on the content already provided in the structure model files in the PDB archive at files.wwpdb.org <https://files.wwpdb.org/>. Read this news online <https://www.wwpdb.org/news/news?year=2023#649f0801d78e004e766a9680> Kind regards, Deborah Harrus PDBe -- ------- 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/
[ccp4bb] wwPDB: NMR restraint remediation conforms to standard NMR-STAR and NEF format
Dear all, NMR data files are standardized in NEF <https://www.nature.com/articles/nsmb.3041> and NMR-STAR format [Ulrich, 2019 <https://link.springer.com/article/10.1007/s10858-018-0220-3>] for the PDB entries which have NMR data in many different software specific formats. This remediation project provides unified NMR data in single NMR-STAR/NEF file for the PDB entries. wwPDB is moving forward single file upload for NMR data (restraints, chemical shifts and possibly peak list) in NMR-STAR/NEF format and will eventually phase out the upload of software specific format in OneDep in future. During this transition period, OneDep converts certain restraint formats into NMR-STAR/NEF at the deposition and provides users with NMR restraint validation <https://www.wwpdb.org/news/news?year=2020#5fc8e8ab09ae2a096d081e27> in wwPDB validation reports for NMR entries having assigned chemical shifts and reasonable restraints in following supported formats: AMBER, BIOSYM, CHARMM, CNS, CYANA, DYNAMO/TALOS/PALES, GROMACS, ISD, ROSETTA, SYBYL, and XPLOR-NIH Depending on complexity of restraints and whether spectral peak lists have been deposited, the first rollout includes NMR entries with simple restraints in the supported formats and without spectral peak lists. The next rollout will include entries with spectral peak lists. Entries which met the following criteria are the scope for remediation: * Both assigned chemical shifts and restraints have been deposited to the PDB * A valid topology file or specific comments must be present to interpret restraint files in a specific format (i.e. AMBER, CHARMM, GROMACS) * All atoms described in NMR data (assigned chemical shifts and restraints) are consistent with model’s atoms * Sequence alignment between the model and restraints matches, allowing terminal sequence extensions NMR-STAR format is the master format used to handle wide variety of restraints in this NMR restraint remediation project. Data items starting with “Auth_asym_ID”, “Auth_seq_ID”, “Auth_comp_ID”, and “Auth_atom_ID” terms, i.e. “_Gen_dist_constraint.Auth_seq_ID_1”, point to equivalent data items in mmCIF, “_atom_site.auth_asym_id”, “_atom_site.auth_seq_id”, “_atom_site.auth_comp_id”, “_atom_site.auth_atom_id”, respectively. Complete atom name mapping information is incorporated using “_Assembly” and “_Entity” categories. NMR constraints used by structure determination software but not covered by the NMR-STAR ontology, such as chemical planarity, equilibrium bond angle, non-crystallographic symmetry, etc., are stored as JSON data under "_Other_constraint_list.text_data" tag to ensure no information is lost during remediation. Furthermore, statistics on remediated restraints are available. NEF data files are provided as best effort conversions from the master NMR-STAR data files. New unified NMR data files in NEF and NMR-STAR formats of existing NMR entries are distributed in the “nmr_data” directory of the PDB archive in the same manner for entries accompanied by the single NMR data file (https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/) and at BMRB archive (https://bmrb.io/ftp/pub/bmrb/nmr_pdb_integrated_data/coordinates_restraints_chemshifts/remediated_restraints). The existing data files in the PDB archive directories “nmr_chemical_shifts” and “nmr_restraints” are remained as is. To retrieve NMR data, users should primarily obtain unified NMR data files at ../nmr_data directory. Conventional chemical shifts and restraints can be used only if unified NMR data are not available. For newly deposited NMR entries with conventional separated NMR data files, OneDep now unifies assigned chemical shifts and restraints into a single data file, which can be accessed from OneDep upload summary page. After submission, depositors can not roll back to the conventional formats. wwPDB validation reports are re-calculated to provide NMR restraint validation for the target entries. NMR restraints can be interpreted and weighted differently by various software during structure calculation. The NMR restraints validation software employs a more general approach recommended by NMR-VTF, independently verifying the satisfaction of each restraint in every model. This can occasionally result in a large number of violations when the actual structure determination software adopts a different approach or assigns less weight during structure calculation. For any further information about NMR data remediation, please contact us at deposit-h...@mail.wwpdb.org. See wwPDB news at https://www.wwpdb.org/news/news?year=2023#64875a3cd78e004e766a967c. Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI
[ccp4bb] wwPDB NEWS: DNS name changes for PDB archive downloads from wwPDB to start September 2023
Dear all, In 2022, wwPDB introduced DNS names <http://www.wwpdb.org/news/news?year=2022#6303be3b707ecd4f63b3d3d9> for programmatic access to PDB archive downloads: * FTP: ftp://ftp.wwpdb.org * HTTPS: https://files.wwpdb.org (replaces https://ftp.wwpdb.org) * RSYNC: rsync://rsync.wwpdb.org (replaces rsync://wwpdb.org) The PDB Archive Downloads <http://www.wwpdb.org/ftp/pdb-ftp-sites> documentation has detailed information. Starting September 2023, wwPDB will start enforcing use of these updated DNS names. URLs in which the DNS name doesn’t match the protocol (e.g., https://ftp.wwpdb.org, ftp://files.wwpdb.org) will no longer work at that time. Users who download PDB archive data programmatically are encouraged to switch to the new DNS names as soon as possible. HTTPS protocol is preferred (over FTP) for individual file downloads. Please contact i...@wwpdb.org with any questions. Read this news online <http://www.wwpdb.org/news/news?year=2023#647631aa1d621d75127a7a54> Kind regards, Deborah Harrus PDBe -- ----------- 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/
[ccp4bb] wwPDB News Update: ls-lR index file in the PDB archive to be removed on July 12, 2023
Dear all, NEW UPDATE: At 00:00 UTC on July 12, 2023, wwPDB will remove the following files from the PDB archive: * ../pdb/ls-lR * ../pdb/data/structures/ls-lR * ../pdb/data/structures/models/ls-lR * ../pdb/data/structures/models/current/ls-lR * ../pdb/data/structures/models/obsolete/ls-lR See details at http://www.wwpdb.org/news/news?year=2023#645bbfdd1d621d75127a7a48 With continuing growth of the PDB archive, the size of the file that lists all directory contents (currently https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. At 00:00 UTC on July 12, 2023, wwPDB will remove the following files from the PDB archive: * ../pdb/ls-lR * ../pdb/data/structures/ls-lR * ../pdb/data/structures/models/ls-lR * ../pdb/data/structures/models/current/ls-lR * ../pdb/data/structures/models/obsolete/ls-lR We strongly encourage users to utilize files previously announced <http://www.wwpdb.org/news/news?year=2021#613b93b3ef055f03d1f222cf> that containing the same data (https://files.wwpdb.org/pub/pdb/holdings/). These inventory data files offer a quick overview of data in the archive. Two new inventory files for experimental data are added. These files are in the extensible JSON format, and can be found under the new /pdb/holdings/ archive tree. The inventory lists provided include: * current_file_holdings.json.gz: a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report). * refdata_id_list.json.gz: a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file. * released_structures_last_modified_dates.json.gz: a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file. * released_experimental_data_last_modified_dates.json.gz: a list of released experimental data files with the most recent modification date * obsolete_structures_last_modified_dates.json.gz: a list of obsoleted PDB entries with the most recent modification date of the PDBx/mmCIF file. * obsolete_experimental_data_last_modified_dates.json.gz: a list of obsoleted experimental data files with the most recent modification date. * all_removed_entries.json.gz: a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any. * unreleased_entries.json.gz: a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available. Users are encouraged to utilize these inventory files. For example, checking for the update of the PDB archive can be performed using current_file_holdings.json.gz <https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz> or released_structures_last_modified_dates.json.gz <https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz> in /pub/pdb/holdings/. Please contact i...@wwpdb.org with any questions. Kind regards, Deborah Harrus PDBe -- ----------- 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/
[ccp4bb] New release of PISA-lite software for calculating macromolecular interaction data
** *Dear all,* * We are excited to announce the release of the new version of the PISA software, developed at PDBe, based on the jsPISA implementation from CCP4. This new version, PISA-lite, developed in collaboration with the CCP4 core team, enables the calculation of macromolecular interaction data for every assembly in the PDB. PISA-lite generates new and enhanced PISA interaction data based on all the annotated assemblies in the PDB archive and is available in JSON format from the PDBe API. It is designed to reduce the computational overhead of the software by working only on known assemblies in PDB entries and calculating interactions. By focusing on known assemblies, PISA-lite enables the weekly calculation of macromolecular interactions for each assembly in the PDB, providing up-to-date information on protein structures and their interactions. These pre-calculated annotations can then be provided for every PDB entry to support researchers in structural biology, bioinformatics, and related fields. To find out more about the PISA-lite implementation and how to access the data, visit:https://www.ebi.ac.uk/pdbe/news/improved-macromolecular-interactions-data-pisa-lite <https://www.ebi.ac.uk/pdbe/news/improved-macromolecular-interactions-data-pisa-lite> Kind Regards, *Deborah Harrus PDBe -- --- 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/
[ccp4bb] wwPDB NEWS: ls-lR index file to be removed July 12, 2023
Dear all, With continuing growth of the PDB archive, the size of the file that lists all directory contents (currentlyhttps://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. wwPDB will remove this file from the PDB archive at 00:00 UTC on July 12, 2023. We strongly encourage users to utilize filespreviously announced <https://www.wwpdb.org/news/news?year=2021#613b93b3ef055f03d1f222cf>that containing the same data (https://files.wwpdb.org/pub/pdb/holdings/). These inventory data files offer a quick overview of data in the archive. Two new inventory files for experimental data are added. These files are in the extensible JSON format, and can be found under the new /pdb/holdings/ archive tree. The inventory lists provided include: * current_file_holdings.json.gz: a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report). * refdata_id_list.json.gz: a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file. * released_structures_last_modified_dates.json.gz: a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file. * released_experimental_data_last_modified_dates.json.gz: a list of released experimental data files with the most recent modification date * obsolete_structures_last_modified_dates.json.gz: a list of obsoleted PDB entries with the most recent modification date of the PDBx/mmCIF file. * obsolete_experimental_data_last_modified_dates.json.gz: a list of obsoleted experimental data files with the most recent modification date. * all_removed_entries.json.gz: a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any. * unreleased_entries.json.gz: a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available. Users are encouraged to utilize these inventory files. For example, checking for the update of the PDB archive can be performed usingcurrent_file_holdings.json.gz <https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz>orreleased_structures_last_modified_dates.json.gz <https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz>in /pub/pdb/holdings/. Please contactinfo@wwpdb.orgwith any questions. Read this news online: https://www.wwpdb.org/news/news?year=2023#645bbfdd1d621d75127a7a48 Kind regards, Deborah Harrus PDBe -- ----------- 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/
[ccp4bb] wwPDB news: Prepare Depositions Using New pdb_extract Features
Dear all, pdb_extract merges coordinate data, author-provided metadata, and data processing information from output files produced by structure determination programs into a complete PDBx/mmCIF file that can used for easy deposition with OneDep. Use the pdb_extract online form <https://pdb-extract.wwpdb.org/> or the easily-installed command line interface <https://sw-tools.rcsb.org/apps/PDB_EXTRACT/source.html> that been re-engineered (Python). Uploaded coordinate files (PDBx/mmCIF or PDB) will be checked against the PDBx/mmCIF dictionary. Legacy PDB formatted files will be converted to a OneDep-compliant PDBx/mmCIF data file. Depositors are encouraged to use the PDBj CIF editor to easily edit a template file to include corresponding metadata (sequence, crystallization condition, etc.). Method-specific templates have been pre-loaded into the PDBj CIF editor: X-ray <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_xray.cif>, 3DEM <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_em.cif>, and NMR <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_nmr.cif>. Click on the top-left menu (light gray widget icon) to save the edited metadata file in PDBx/mmCIF. Upload this completed file in pdb_extract to prepare single or multiple related structures for submission. Upload the log file produced during data processing, and pdb_extract will parse the related diffraction metadata. Log files from various standalone packages and from CCP4 and autoPROC pipelines are supported, including: Aimless DIALS d*TREK HKL-2000 HKL-3000 Pointless Scala Scalepack XDS Xia2 Xscale Read this news online <http://www.wwpdb.org/news/news?year=2023#6455391c1d621d75127a7a46> Kind regards, Deborah. -- ------- 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/
[ccp4bb] wwPDB NEWS: Access Depositions Using ORCiD
Dear all, We are pleased to announce that contact authors can now useORCiDs <https://orcid.org/>to authenticate OneDep access. This authentication method allows each contact author to login to OneDep without the need for password sharing to view and access all their depositions. OneDep login using a deposition ID and password is still possible, but will only provide access to the specific deposition. Using ORCiD with OneDep returns a summary table of the entries in which the ORCiD has been provided for the contact author. Users can further access each of their entries’ deposition interfaces without the need to login again using a deposition ID or password. The ORCiD sign-in button is located below the existing login fields./The ORCiD sign-in button is located below the existing login fields./ After using the ORCiD login, this OneDep panel will displaying all available depositions. <https://cdn.rcsb.org/news/2023/onedeporcidpanel.png>/After using the ORCiD login, this OneDep panel will displaying all available depositions./ First-time OneDep contact authors will need to verify their email address before being able to create new depositions, similar to creating a new deposition without being logged-in with ORCiD. Please be aware that adding a contact author ORCiD in the “Admin > Contact information” OneDep page will grant this author access to the current deposition. Providing ORCiDs for OneDep contact authorshas been mandatory since 2018 <https://www.wwpdb.org/news/news?year=2018#5b2ced769ea23a2bf4a27b1d>. Read this news online: https://www.wwpdb.org/news/news?year=2023#641872ffe0a2cc03bf315460 Kind regards, Deborah Harrus PDBe -- ----------- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] wwPDB News: PDB entries with extended CCD or PDB IDs will be distributed in PDBx/mmCIF format only
Dear all, As announced previously, wwPDB, in collaboration with thePDBx/mmCIF Working Group <https://www.wwpdb.org/task/mmcif>, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by the legacy PDB file format. (see previous announcement <https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d>: https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d) CCD ID extension CCD entries are currently identified by unique three-character alphanumeric IDs. At current growth rates, we anticipate running out of three-character IDs before 2024. After this point, the wwPDB will issue*five-character alphanumeric accession codes for CCD IDs*in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes will not be used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes will only be distributed in PDBx/mmCIF format. In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB. These reserved codes can be used for new ligands during structure determination so that they can be identified as new upon deposition and added to the CCD during biocuration. PDB ID extension wwPDB will be extending PDB ID length to eight characters prefixed by ‘pdb’, e.g., pdb_1abc. Each PDB entry has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors. Extended PDB IDs and corresponding PDB DOIs have been included in the PDBx/mmCIF formatted atomic coordinate files for all new and re-released entries since August 2021. For example, PDB entry issued with 4-character PDB ID, 1abc, will have the extended PDB ID (pdb_1abc) and corresponding PDB DOI (10.2210/pdb1abc/pdb), as listed in the _database_2 PDBx/mmCIF category. loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1abc pdb_1abc 10.2210/pdb1abc/pdb For example, PDB entry issued with 8-character PDB ID, pdb_00099xyz, after all 4-character IDs are consumed: loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB pdb_00099xyz pdb_00099xyz 10.2210/pdb_00099xyz/pdb After all four-character PDB IDs are consumed, newly-deposited PDB entries will only be issued extended PDB ID codes, and PDB entries will only be distributed in PDBx/mmCIF format. PDB entries with four-character PDB IDs will remain unchanged. Resources wwPDB is asking users and software developers to review their code and remove any current limitations on PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended PDB and/or CCD IDs are available via github to assist code revisions, seehttps://github.com/wwPDB/extended-wwPDB-identifier-examples. To learn about PDBx/mmCIF, please visithttps://mmcif.wwpdb.org/. For any further information please contact us ati...@wwpdb.org. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7 Kind regards, Deborah. -- ------- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] wwPDB news: Small Angle Scattering News
Dear all, An outcome of a project aimed to test and benchmark different approaches for modeling SAS profiles from PDB coordinates has been published: *A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking* Trewhella, J., Vachette, P., Bierma, J., Blanchet, C., Brookes, E., Chakravarthy, S., Chatzimagas, L., Cleveland, T. E., Cowieson, N., Crossett, B., Duff, A. P., Franke, D., Gabel, F., Gillilan, R. E., Graewert, M., Grishaev, A., Guss, J. M., Hammel, M., Hopkins, J., Huang, Q., Hub, J. S., Hura, G. L., Irving, T. C., Jeffries, C. M., Jeong, C., Kirby, N., Krueger, S., Martel, A., Matsui, T., Li, N., Perez, J., Porcar, L., Prange, T., Rajkovic, I., Rocco, M., Rosenberg, D. J., Ryan, T. M., Seifert, S., Sekiguchi, H., Svergun, D., Teixeira, S., Thureau, A., Weiss, T. M., Whitten, A. E., Wood, K. & Zuo, X. (2022)/Acta Cryst./D78: 1315-1336 doi:10.1107/S2059798322009184 <https://doi.org/10.1107/S2059798322009184> In total, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were collected and analyzed centrally. In the process, new methods for data comparing and merging were developed. The data produced for this effort, has been deposited in theSAS Biological Data Bank (SASBDB) <https://www.sasbdb.org/>as consensus data along with the contributing individual data sets. In addition, a chapter describing the work done to establish the 2017 publication guidelines for biomolecular SAS, the establishment of the SASBDB, and the evolution and outcomes of the bench-marking project has been published: *Chapter One - Data quality assurance, model validation, and data sharing for biomolecular structures from small-angle scattering* Jill Trewhella (2023)/Methods in Enzymology/678: 1-22 doi:10.1016/bs.mie.2022.11.002 <https://doi.org/10.1016/bs.mie.2022.11.002> These publications reflect the activities of thewwPDB Small Angle Scattering task force (SAStf) <https://www.wwpdb.org/task/sas>that first met with Chair Jill Trewhella in 2012. The SAStf was instrumental in progressing the important work that has led to biomolecular SAS being increasingly accepted as a mainstream structural biology technique. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d97fafc031758bf1c30fed Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available
Dear all, A prototype of a next generation archive repository for the PDB is now available. The archive, called “NextGen”, hosts structural model files in PDBx/mmCIF and PDBML formats atfiles-nextgen.wwpdb.org <https://files-nextgen.wwpdb.org/>. This enriched PDB archive provides annotation from external database resources in the metadata in addition to the content provided in the structure model files in the PDB main archive atfiles.wwpdb.org <https://files.wwpdb.org/>. This prototype provides sequence annotation from external resources such as UniProt, SCOP2 and Pfam at atom, residue, and chain levels. This mapping information is derived from the Structure Integration with Function, Taxonomy and Sequence (SIFTS) project (https://www.ebi.ac.uk/pdbe/docs/sifts/), a service developed and maintained by the PDBe and UniProt teams at EMBL-EBI. Sequence mappings are provided in _pdbx_sifts_unp_segments and _pdbx_sifts_xref_db_segments categories for each segment, _pdbx_sifts_xref_db at residue level, and _atom_site at atom level. The PDB NextGen Repository is currently updated monthly on the first Wednesday of the month at 00:00 UTC and is subject to change in the future. You can access these NextGen files at the following locations: * wwPDB:https://files-nextgen.wwpdb.org, rsync://rsync-nextgen.wwpdb.org * RCSB PDB (USA):https://files-nextgen.rcsb.org, rsync://rsync-nextgen.rcsb.org * PDBe (UK):https://ftp.ebi.ac.uk/pub/databases/pdb_nextgen/ * PDBj (Japan):https://ftp-nextgen.pdbj.org <https://www.wwpdb.org/news/news?year=2023> Data are structured based on entry ID with a two letter hash code, ‘third from last character' and 'second from last character’. This hash code will remain consistent once PDB ID codes are extended beyond four characters with the pdb_ prefix. Some examples are shown below: * Access entry pdb_8aly athttps://files-nextgen.wwpdb.org/pdb_nextgen/data/entries/divided/al/pdb_8aly/ * Both PDBx/mmCIF and PDBML are provided at this location. For entry pdb_8aly: o pdb_8aly_xyz-enrich.cif.gz o pdb_8aly_xyz-no-atom-enrich.xml.gz Please contactinfo@wwpdb.orgwith any questions. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63cedad9b5f08ee94ab73826 Kind regards, Deborah Harrus PDBe -- ----------- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Structure Predictors: Use ModelCIF for Computed Structure Models
Dear all, ModelCIF (GitHub <http://github.com/ihmwg/ModelCIF>) is a data information framework developed for and by computational structural biologists to describe structural models of macromolecules derived from computational methods. It provides an extensible data representation for deposition, archiving, and public dissemination of these models of proteins to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. A. Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic representation of ModelCIF data specifications. ModelCIF includes definitions for input data used in template-based and template-free modeling; reference information for macromolecular sequences and small molecule components; local and global CSM quality metrics; and metadata information regarding modeling protocol, CSM classification (ab initio, homology, etc.) and descriptions of associated files. <https://cdn.rcsb.org/news/2023/modelcifextensionofpdbx-mmcif.png>/A. Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic representation of ModelCIF data specifications. ModelCIF includes definitions for input data used in template-based and template-free modeling; reference information for macromolecular sequences and small molecule components; local and global CSM quality metrics; and metadata information regarding modeling protocol, CSM classification (ab initio, homology, etc.) and descriptions of associated files./ ModelCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF <https://mmcif.wwpdb.org/>), which is the global data standard for representing experimentally-determined, three-dimensional (3D) structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the wwPDB in collaboration with relevant community stakeholders such as thewwPDB ModelCIF Working Group <https://www.wwpdb.org/task/modelcif>. This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Furthermore, use of this data standard promotes inter-operation among structural biology data resources, with ModelCIF currently used by theModelArchive <https://www.modelarchive.org/>,AlphaFold DB <https://alphafold.ebi.ac.uk/>, andMODBASE <https://modbase.compbio.ucsf.edu/>repositories. A manuscript was recently submitted to/bioRxiv/ <https://doi.org/10.1101/2022.12.06.518550>describing the architecture, contents, and governance of ModelCIF as well as tools and processes for maintaining and extending the data standard [1]. Visit theModelCIF GitHub <http://github.com/ihmwg/ModelCIF>for more information about this data information framework. [1] Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, et al. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models./bioRxiv/doi:10.1101/2022.12.06.518550 <https://doi.org/10.1101/2022.12.06.518550>. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d28b2c314f0e7e1b1d3ce6 Kind regards, Deborah Harrus PDBe -- ------- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Enhanced Collection of Starting Models
Dear all, A new PDBx/mmCIF category, _pdbx_initial_refinement_model has been introduced to improve information collected about starting model for X-ray, 3DEM and NMR methods. Experimentally derived vs computed models will be distinguished. Provenances of the resources where the starting model was obtained (e.g., PDB, AlphaFoldDB, RoseTTAFold, etc.) and its accession code/identifier will be captured, if publicly available. For the full definition, see pdbx_initial_refinement_model>. An example is below: _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list 1 _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3LTQ wwPDB strongly recommends all PDB users and software developers to review their code and adopt this definition for future applications. Read this news on the wwPDB website: https://www.wwpdb.org/news/news?year=2023#63d97981c031758bf1c30fec Kind regards, Deborah Harrus PDBe -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] PDB Reaches a New Milestone: 200,000+ Entries
Dear all, With this week's update, the PDB archive contains a record 200,069 entries. The archive passed 150,000 structures in 2019 and 100,000 structures in 2014. Established in 1971, this central, public archive has reached this critical milestone thanks to the efforts of structural biologists throughout the world who contribute their experimentally-determined protein and nucleic acid structure data. wwPDB data centers support online access to three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy. Many milestones have been reached since the archive released the 100,000th structure in 2014. PDB data have been seminal in understanding SARS-CoV-2, and provided the foundation for the development of AI/ML techniques for predicting protein structure. The 50th anniversary of the PDB was celebrated throughout 2021. Today, the archive is quite large, containing more than 3,000,000 files related to these PDB entries that require more than 1086 Gbytes of storage. PDB structures contain more than 1.8 billion non-hydrogen atoms. In the 1950s, scientists had their first direct look at the structures of proteins and DNA at the atomic level. Determination of these early three-dimensional structures by X-ray crystallography ushered in a new era in biology-one driven by the intimate link between form and biological function. As the value of archiving and sharing these data were quickly recognized by the scientific community, the Protein Data Bank (PDB) was established as the first open access digital resource in all of biology by an international collaboration in 1971 with data centers located in the US and the UK. Among the first structures deposited in the PDB were those of myoglobin and hemoglobin, two oxygen-binding molecules whose structures were elucidated by Chemistry Nobel Laureates John Kendrew and Max Perutz. With this week's regular update, the PDB welcomes 266 new structures into the archive. These structures join others vital to drug discovery, bioinformatics and education. The PDB is growing rapidly, increasing in size ~13% since 2011. In 2022, an average of 275 new structures were released to the scientific community each week. The resource is accessed hundreds of millions of times annually by researchers, students, and educators intent on exploring how different proteins are related to one another, to clarify fundamental biological mechanisms and discover new medicines. Since its inception, the PDB has been a community-driven enterprise, evolving into a mission critical international resource for biological research. The wwPDB partnership was established in July 2003 with PDBe, PDBj, and RCSB PDB. Today, the collaboration includes partners BMRB (joined in 2006) and EMDB (2021). The wwPDB ensures that these valuable PDB data are securely stored, expertly managed, and made freely available for the benefit of scientists and educators around the globe. wwPDB data centers work closely with community experts to define deposition and annotation policies, resolve data representation issues, and implement community validation standards. In addition, the wwPDB works to raise the profile of structural biology with increasingly broad audiences. Each structure submitted to the archive is carefully curated by wwPDB staff before release. New depositions are checked and enhanced with value-added annotations and linked with other important biological data to ensure that PDB structures are discoverable and interpretable by users with a wide range of backgrounds and interests. wwPDB eagerly awaits the next 100,000 structures and the invaluable knowledge these new data will bring. Read more: https://www.wwpdb.org/news/news?year=2023#639b9e337f8444f313d20414 Kind regards, Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Deprecation of FTP File Download Protocol in the PDB Archive
Dear all, The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web browsers (Chrome and Firefox) have dropped support for the FTP protocol, which has effectively discontinued the FTP protocol for non-technical users. Given that the majority of file download activity on the internet has moved to HTTP/S, wwPDB plans to deprecate FTP download protocol on November 1st 2024. wwPDB has traditionally supported FTP, together with HTTP/S and RSYNC. Gradual deprecation of the FTP protocol, in favor of the HTTP/HTTPS protocol will be approached while maintaining support for the RSYNC protocol which offers additional functionality compared to the other 2 protocols. As announced previously (http://www.wwpdb.org/news/news?year=2022#6303be3b707ecd4f63b3d3d9), we have introduced DNS names that are specific to the protocols: * files.wwpdb.org for HTTP/S * ftp.wwpdb.org for FTP. To be deprecated on November 1st 2024. Note that from September 2023 this DNS name will not accept HTTP/S traffic. * rsync.wwpdb.org for RSYNC Starting September 2023, wwPDB will start enforcing use of these updated DNS names for the preparation of FTP protocol deprecation. Please contact i...@wwpdb.org with any questions. Kind regards, Deborah Harrus PDBe -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] AlphaFold DB models superposed on PDB structures at PDBe-KB
** *Dear colleagues,* * We have expanded the superposition process at the PDBe-KB aggregated views of proteins to allow superposition of the predicted model from the AlphaFold Protein Structure Database (AlphaFold DB). This new feature loads the model from AlphaFold DB on demand and superposes it to the equivalent PDB structures, using the superposition functionality through the Mol* molecular viewer. This allows easy comparison of the different conformational states of a given protein in the PDB with the models predicted in AlphaFold DB, to identify if the predicted model represents a specific conformational state. You can view the structure superposition for a specific protein (per UniProt accession) at the PDBe-KB aggregated views of proteins (pdbekb.org/protein). The superposition can be accessed from the Summary or Structures tabs using the green buttons labelled ‘3D view of superposed structures’. Read more at https://www.ebi.ac.uk/pdbe/news/compare-experimental-models-pdb-alphafold-models-pdbe-kb Kind Regards, *Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] wwPDB Charter: Full and Associate Members
Dear all, Founded in 2003, the Worldwide Protein Data Bank (wwPDB) is dedicated to archiving, management, and public dissemination of structural biology data, and is committed to the FAIR Principles (Findability, Accessibility, Interoperability, Reusability) that are emblematic of responsible stewardship of public domain information. wwPDB operations are governed by the wwPDB Charter (which can be read at: https://cdn.rcsb.org/wwpdb/img/about/2021_wwPDB_Charter_with_Appendix.pdf), which was most recently renewed in 2021. The renewed agreement provides for two types of wwPDB membership--Full and Associate. Current wwPDB Full Members include three founding members [Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, USA), Protein Data Bank in Europe (PDBe, United Kingdom), and Protein Data Bank Japan (PDBj, Japan)] and two specialist data resource members [Biological Magnetic Resonance Bank (BMRB, USA and Japan; joined in 2006) and Electron Microscopy Data Bank (EMDB, United Kingdom; joined in 2021)]. Full Members jointly manage three wwPDB Core Archives, including the Protein Data Bank, the Biological Magnetic Resonance Bank, and the Electron Microscopy Data Bank. Data safety and security and periodic archival updates are the primary responsibility of three wwPDB-designated Archive Keepers, including RCSB PDB for the Protein Data Bank, BMRB for the Biological Magnetic Resonance Bank, and EMDB for the Electron Microscopy Data Bank. The wwPDB acknowledges the importance of global equity in the ability to deposit and access data, and the need for international involvement and collaboration in maintaining the wwPDB Core Archives. The renewed wwPDB Charter describes the Associate Membership program, wherein Associate Members are expected to contribute to some of the wwPDB activities (deposition, validation, biocuration, remediation, storage, dissemination of public-domain structural biology data stored in one or more wwPDB Core Archives). The responsibilities of an individual wwPDB Associate Member for deposition, validation, biocuration, remediation, storage, and/or dissemination of public-domain structural biology data stored in one or more wwPDB Core Archives must be agreed upon by all wwPDB Full Members. At the discretion of wwPDB Full Members, an external organization may be invited to apply to become a wwPDB Associate Member, following preliminary discussions and successful completion of due diligence and demonstration of sufficient technical expertise, adequate infrastructure, and sustainable funding. The decision to admit a new wwPDB Associate Member must be by unanimous vote of the current Heads of the existing wwPDB Full Members, supported by a simple majority of the voting members of the wwPDB Advisory Committee. Full details of the arrangement are provided in the wwPDB Charter (read at: https://cdn.rcsb.org/wwpdb/img/about/2021_wwPDB_Charter_with_Appendix.pdf). Kind regards, Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Improved EM validation with Q-score
Dear all, As announced previously, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will now include the Q-score metric (Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations from the wwPDB/EMDB workshop on cryo-EM data management, deposition and validation in 2020 (white paper in preparation), as well as EM Validation Challenge events (Lawson C., et al., 2020, Struct. Dyn.; Lawson, et al., 2021, Nat. Methods). This will be the first quantitative parameter of residue and chain resolvability for EM maps in wwPDB validation reports and will provide an additional map-model assessment criterion. The Q-score calculates the resolvability of atoms by measuring similarity of the map values around each atom relative to a Gaussian-like function for a well resolved atom. Q-score of 1 indicates that the similarity is perfect whilst closer to 0 indicates the similarity is low. If the atom is not well placed in the map then a negative Q-score value may be reported. Therefore, Q-score values in the reports will be in a range of -1 to +1. The wwPDB EM validation reports will provide Q-scores for single particle, helical reconstruction, electron crystallography and subtomogram averaging entries for which both an EM map and coordinate model have been deposited. Validation reports (PDF files) will contain images of the average per-residue Q-scores color-mapped onto ribbon models with views from three orthogonal directions. Similar images will also be introduced to visualize the per-residue atom-inclusion scores. Comparison of these two sets of images will assist in visual assessment of the model-to-map fit and quality. To see example images of models where residues are colored according to their Q-score, please visit the news page on the wwPDB website: http://www.wwpdb.org/news/news?year=2022#63288a46831916e52206a1f0 The validation reports will also contain a table of average per-chain values of both metrics (Q-score and atom inclusion) as well as their overall average values for the entire model. The per-residue and the per-chain average atom-inclusion and Q-score values will also be provided in the mmCIF and XML formatted validation files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and _pdbx_vrpt_model_instance_map_fitting will be introduced to include both the Q-scores and atom-inclusion values. The existing items, _pdbx_vrpt_summary_entity_geometry.average_residue_inclusion (https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion.html) and _pdbx_vrpt_model_instance_geometry.residue_inclusion (https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_model_instance_geometry.residue_inclusion.html) for atom inclusion will no longer be used. The PDB Core Archive holds validation reports that assess each 3DEM model in the PDB along with the associated experimental 3D volume in EMDB. Validation reports of 3DEM structures (map and model) can be downloaded at the following wwPDB mirrors: - wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/ - RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/ - PDBe: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ - PDBj: https://ftp.pdbj.org/pub/pdb/validation_reports/ The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. Validation reports for all EMDB volumes can be downloaded at the following wwPDB mirrors: - EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/ - wwPDB: https://ftp.wwpdb.org/pub/emdb/validation_reports/ - RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/ - PDBj: https://ftp.pdbj.org/pub/emdb/validation_reports/ Additional information about validation reports is available: - for EM map+model: http://www.wwpdb.org/validation/2017/EMValidationReportHelp - EM map-only: http://www.wwpdb.org/validation/2017/EMMapValidationReportHelp - EM tomograms: http://www.wwpdb.org/validation/2017/EMTomogramValidationReportHelp If you have any questions or queries about wwPDB validation, please contact us at validat...@mail.wwpdb.org. Kindest regards, Deborah Harrus. -- --- Deborah Harrus, Ph.D. Lead Annotator 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 avail
[ccp4bb] PDB entries with extended CCD or PDB IDs will be distributed in the PDBx/mmCIF format only
Dear all, wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by the legacy PDB file format. (see previous announcement here: https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d) CCD entries are currently identified by unique three-character alphanumeric IDs. At current growth rates, we anticipate running out of three-character IDs before 2024. After this point, the wwPDB will issue five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes will not be used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes will only be distributed in PDBx/mmCIF format. In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB. These reserved codes can be used for new ligands during structure determination so that they can be identified as new upon deposition and added to the CCD during biocuration. wwPDB will be extending PDB ID length to eight characters prefixed by ‘pdb’, e.g., pdb_1abc. Each PDB entry has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals and described in publications by the structure authors. Extended PDB IDs and corresponding PDB DOIs have been included in the PDBx/mmCIF formatted atomic coordinate files for all new and re-released entries since August 2021. For example, PDB entry issued with 4-character PDB ID, 1abc, will have the extended PDB ID (pdb_1abc) and corresponding PDB DOI (10.2210/pdb1abc/pdb), as listed in the _database_2 PDBx/mmCIF category. loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1abc pdb_1abc 10.2210/pdb1abc/pdb For example, PDB entry issued with 8-character PDB ID, pdb_00099xyz, after all 4-character IDs are consumed: loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB pdb_00099xyz pdb_00099xyz 10.2210/pdb_00099xyz/pdb After all four-character PDB IDs are consumed, newly-deposited PDB entries will only be issued extended PDB ID codes, and PDB entries will only be distributed in PDBx/mmCIF format. PDB entries with four-character PDB IDs will remain unchanged. wwPDB is asking users and software developers to review their code and remove any current limitations on PDB and CCD ID lengths, and to enable use of PDBx/mmCIF format files. Example files with extended PDB and/or CCD IDs are available via github to assist code revisions, see https://github.com/wwPDB/extended-wwPDB-identifier-examples. To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/. For any further information please visit https://www.wwpdb.org/news/news?year=2022#630fee4cebdf34532a949c34 or contact us at i...@wwpdb.org. Kindest regards, Deborah Harrus -- --- Deborah Harrus, Ph.D. Lead Annotator 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] Regarding Protein biological assembly
Dear Abhilash, Starting May 3, 2022, the PDB archive distributes assembly files in PDBx/mmCIF format. You can access the files here: ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/ Alternatively, you can use the PDBe download service: https://www.ebi.ac.uk/pdbe/download/ You could retrieve the files and then convert them using MAXIT (you could make a simple script to run them in batches)? May I ask for which purpose do you need files in PDB format instead of mmCIF format? Kind regards, Deborah Harrus PDBe On 11/07/2022 05:30, Abhilasha Thakur wrote: Hello, I have a long list of PDB ids and I needed the all the biological assembly for each PDB Id, so in this case how I can get these biological assembly in PDB format. Please guide me how to get these assemblies, manually it wouldn't be possible for each PDB I'd. Thankyou To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- --- Deborah Harrus, Ph.D. Lead Annotator 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] wwPDB_Deposition errors
Dear Anton, May I suggest that you contact the wwPDB directly through the "Communication" tab of your deposition session? We'll then be able to look at your files and advise you. Kind regards, Deborah PDBe On 18/07/2022 08:39, Anton Hamann wrote: Hello I'm having some trouble uploading the mmCIF files to the wwPDB_deposition from PDB_Extract. The 2 errors are as follow: Critical Data Values: Structure factor file is missing freeR set. PDB format issues: Chain IDs contain more than one character. How can I fix these errors? Thank you for your help. Regards Anton 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. Lead Annotator 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/
[ccp4bb] (reminder) Scientific Data Curator position (PDB and EMDB)
Dear all, This is a kind reminder that we are looking to recruit an expert structural biologist to join the PDBe curation team on the Wellcome Genome Campus near Cambridge. The work involves annotating preliminary PDB and EMDB submissions and extracting relevant biological information. The closing date for the post is 17th July 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI02041 If you are you an expert structural biologist looking for something new but still wanting to have a great impact in your field, this is a great opportunity! Kind Regards, Deborah -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Scientific Data Curator position (PDB and EMDB)
Dear all, We are looking to recruit an expert structural biologist to join the PDBe curation team on the Wellcome Genome Campus near Cambridge. The work involves annotating preliminary PDB and EMDB submissions and extracting relevant biological information. The closing date for the post is 17th July 2022. For more information on the position, please visit: https://www.embl.org/jobs/position/EBI02041 Kind Regards, Deborah -- --- Deborah Harrus, Ph.D. Lead Annotator 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/
[ccp4bb] Distributing PDBx/mmCIF-Formatted Assembly Files
Dear all, Starting May 3, 2022, the PDB archive distributes assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries (original announcement <https://www.wwpdb.org/news/news?year=2022#61f7f8bc8f40f9265109d398>). Previously, PDBx/mmCIF formatted assembly files provided for structures were non-PDB compliant, however the coordinates use model numbers to differentiate alternate symmetry copies of PDB chain IDs. This method is not ideal, nor necessary, for the current archive PDBx/mmCIF format and has led to limited use of these files in community software tools. In response to this issue and recommendations by the wwPDB advisory committee, we are implementing updated, standardized practices for generation of assembly files for all PDB entries. These updated PDBx/mmCIF format assembly files have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules: Chain IDs of the original chains from the atomic coordinate file will be retained (e.g., A) Assign unique chain ID (atom_site.label_asym_id and atom_site.auth_asym_id) for each symmetry copy within a single model. Rules of chain ID assignments: The applied index of the symmetry operator (pdbx_struct_oper_list.id) will be appended to the original chain ID separated by a dash (e.g., A-2, A-3, etc.) If there are more than one type of symmetry operators applied to generate symmetry copy, a dash sign will be used between two operators (e.g., A-12-60, A-60-88, etc.) In addition, entity ID and chain ID mapping categories are provided: _pdbx_entity_remapping and _pdbx_chain_remapping. A new directory (https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/) was created for the distribution of these updated assembly files. The directory containing the existing assembly mmCIF files for large entries has been removed (ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/'>ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/). wwPDB asks all PDB users and software developers to review code and address any limitations related to PDB assemblies. Sample files were made available for testing purposes and to support community adoption at GitHub.com/wwpdb/assembly-mmcif-examples <https://github.com/wwpdb/assembly-mmcif-examples>. If you plan to use these assembly files for graphical viewing, check if your visualization software (e.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), for improved efficiency. For any further information please email i...@wwpdb.org. Kind regards, Deborah Harrus -- ------- Deborah Harrus, Ph.D. Lead Annotator PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK dhar...@ebi.ac.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] How to fit BioSAXS shape to the Structure
Dear Weifei, You might want to use SUPCOMB from the ATSAS suite. http://www.embl-hamburg.de/biosaxs/supcomb.html Cheers, Deborah.
Re: [ccp4bb] Seeking software for Dynapro 99 DLS
Dear Ho, I have an old version of Protein Solution (pre-Wyatt) Dynamics CD-ROM including Dynamics version 5.25.44 and everything (manuals, drivers, ...). The whole package is around 80 Mo. Let me know if it's what you are searching for, and I will upload it somewhere so you can retrieve it. Have a nice day, Deborah. -- Deborah Harrus, PhD Post-doctoral fellow Team 3-1 Nuclear Receptors and Epigenetics Centre de Biochimie Structurale CNRS UMR5048 / INSERM U1054 29 rue de Navacelles 34090 Montpellier, France Phone: 04 67 41 77 19 - Mail original - De: Ho Leung Ng h...@hawaii.edu À: CCP4BB@JISCMAIL.AC.UK Envoyé: Samedi 2 Août 2014 09:26:40 Objet: [ccp4bb] Seeking software for Dynapro 99 DLS Hi, Can someone help me with obtaining the software to operate a Dynapro 99 DLS instrument? Wyatt no longer provides software for this model. Newer versions of Dynamics are not compatible with the Dynapro 99. Thank you! Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
Re: [ccp4bb] Script for Comparing Structurally-Similar Proteins
Hi, I love using the ESCET algorithm developed by Thomas R. Schneider, it calculates error-scaled difference distance matrices, identifies domains very precisely, generates pml of aligned and coloured molecules... I just love it. More info: http://www.ncbi.nlm.nih.gov/pubmed/10818348 http://www.ncbi.nlm.nih.gov/pubmed/11807243 http://www.ncbi.nlm.nih.gov/pubmed/15572780 Cheers, Deborah. -- Deborah Harrus, PhD Nuclear Receptors and Epigenetics Centre de Biochimie Structurale CNRS UMR5048 / INSERM U1054 Montpellier, France - Mail original - De: Jacob Keller kell...@janelia.hhmi.org À: CCP4BB@JISCMAIL.AC.UK Envoyé: Mardi 6 Mai 2014 16:49:22 Objet: [ccp4bb] Script for Comparing Structurally-Similar Proteins Dear Crystallographers, In a former lab we had a script which would read DALI output, automatically download the structurally-similar proteins, superimpose them, and color by regions superimposed. That was in the days of O. Does anyone have a similar-functioning script for CCP4MG, pymol, or other software that I could use? I find myself often building such superpositions manually, and this must be a pretty common endeavor... Thanks, Jacob *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
