Dear Frank
We are working together with the mmCIF working group on exactly this. mmCIF’s from phenix and refmac have parameters of the dictionaries used in refinement as additional data blocks. We are currently making sure that the output is identical from both packages so we can use it later. John From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 12 November 2018 09:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Very strange LINK cards appearing in recent structures Sorry, that was menat to be: "... force us to deposit full details...." On 12/11/2018 09:49, Frank von Delft wrote: While you're at it, can you force us full details of restraints used, whether it's the particular CCP4 library release, the CIF of the ligand, or the non-standard links? As far as I understand refinement, they're as least as important a determinant of the final structure as the observed data. phx On 12/11/2018 09:44, John Berrisford wrote: Dear all We (the wwPDB) are actively looking into and correcting link records in the PDB. A lot of the recent re-releases were (and will continue to be) to correct links in existing PDB entries. I removed over 10,000 incorrect links in one sitting! We are also working to ensure that incorrect link records do not get added into entries during annotation and part of this process is working with developers of refinement packages to ensure that we receive links as they were used in refinement in a standard format that we can read. As Robbie mentioned, if you do find any entries with incorrect link records then do please let us know so we can correct them. Regards John PDBe -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clemens Vonrhein Sent: 12 November 2018 07:32 To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Very strange LINK cards appearing in recent structures Dear all, we also have a lot of "fun" with LINK records when taking deposited PDB structures into BUSTER refinement. Sometimes (but not often) there are missing LINK records, but the vast number of problems is due to erroneous LINK records added by annotation software it seems (based on a cut-off of 3.5A apparently). Correcting those issues once reported is one option, but maybe revisiting the idea about auto-generating LINK records during deposition would be beneficial. At the end of refinement the various packages will have all required and no wrong/additional LINK records in the final PDB file - and deposition software should probably take those as-is without automatically rewriting/adding/removing any (while still present a note/warning to depositor about potentially missed LINK records according to annotation software). This would most likely result in much fewer LINK problems in deposited PDB structures. As the format guide says: The LINK records specify connectivity between residues that is not implied by the primary structure. and specifically mentions bonds (not hydrogen bonds or salt-bridges): https://www.wwpdb.org/documentation/file-format-content/format33/sect6.html# <https://www.wwpdb.org/documentation/file-format-content/format33/sect6.html> LINK Cheers Clemens On Sun, Nov 11, 2018 at 07:31:55PM +0000, Robbie Joosten wrote: Erroneous LINK records happen quite a lot and used to be the combination of aggressive annotation software and depositors not paying attention to the comments from the annotators. They make up a large fraction of the bug reports I have sent to the PDB over the years. They are usually fixed very quickly by the annotators, as long as someone takes time to report them. This case looks like an error in a refinement program which nevertheless should have been caught by the depositors. What I would like to know is whether the deposited, pre-annotation model had the LINKs or not. LINKs are a bloody nightmare when it comes to annotation. At the moment there is no record keeping of targets and chemical modifications in a dictionary on the side of the PDB so there is also no standardisation. IMO mmCIF makes it easier to store the restraints with the coordinates, but there is still no neat mapping by LINK identfiers the way the LINKR format works in Refmac. I think that is a missed opportunity. Sorry for the rant, I blame the F1. Cheers, Robbie Op 11 nov. 2018 19:47 schreef Tristan Croll <mailto:ti...@cam.ac.uk> <ti...@cam.ac.uk>: I've seen instances like the following in roughly half a dozen deposited structures over the past year or so. Each time I've contacted the authors, who've been just as mystified as me by them - and certainly didn't add them on purpose. It seems to me that some fairly commonly-used package is erroneously turning clashes into LINK cards in some circumstances. I just found the following clearly wrong LINKs in 6caj (deposited January this year): LINK CD2 PHE I 266 CG2 THR I 272 1555 1555 1.47 LINK CE2 PHE I 266 CG2 THR I 272 1555 1555 1.47 ... which looks like the attached image. The same bonds are also specified in the mmCIF file, for the record. Anyone have any clue? Best regards, Tristan ###################################################################### ## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ###################################################################### ## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
