Yes, but when the validation reports are as comprehensive as this<http://www.wwpdb.org/validation/validation-reports.php>, it's all too easy to assume that they've covered all possible issues and that the lack of a list of cis bonds means there are none. I understand that the next release of MolProbity will include this in its suite of checks so the issue should begin to go away as people upgrade.
Cheers, Tristan ________________________________ From: Bernhard Rupp <hofkristall...@gmail.com> on behalf of Bernhard Rupp <b...@ruppweb.org> Sent: Monday, 16 February 2015 8:55 PM To: Tristan Croll; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Cis-peptide bond checking Hmm....CISPEP records are provided... CISPEP 1 GLY A 63 LEU A 64 0 1.59 CISPEP 2 LEU A 69 PRO A 70 0 -14.05 CISPEP 3 PRO A 70 PRO A 71 0 -2.41 CISPEP 4 ASP A 162 GLY A 163 0 -8.79 Which can be parsed/checked.... ....but then again, who does? https://www.youtube.com/watch?v=bAZqE2DnxUI Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tristan Croll Sent: Montag, 16. Februar 2015 10:58 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cis-peptide bond checking Dear all, My apologies for the spam-like nature of my post, but I would like to draw your attention to an important issue (outlined in an upcoming short communication to Acta D, which will appear at doi:10.1107/S1399004715000826 once it's online). At present, neither the structural quality checks in commonly-used crystallography packages nor those run on deposition of a structure to the PDB are flagging the presence of non-proline cis peptide bonds. This has led to the presence of many erroneous cis bonds creeping into the PDB - primarily in low-resolution structures as one would expect, but I have identified clearly erroneous examples in structures with resolutions as high as 1.3 Angstroms. From my analysis, I estimate that a few thousand structures have been affected to some extent, with the worst cases having as high as 3% of their peptide bonds in cis. Particularly if you have published anything >2.5 Angstroms in the past few years, may I gently suggest that you make a quick double-check of your deposited structures? This can be done quickly and simply in Coot (Extensions-Modelling-Residues with Cis peptide bonds). Best regards, Tristan
