Re: [ccp4bb] Puzzling Structure
Hi Martyn, >I think the question is where the error was made - seeing the uploaded file > would clear this up. But it seems unlikely to me that the depositor saw a huge > R factor discrepancy at the end of refinement and just blithely uploaded it. > So scenario 3 :- > PDB : we cannot reproduce your R factor with our programs > Depositor : that's your problem mate - it was fine when it left me...up to > you to sort it... >Which seems a sort of reasonable attitude to me. Not quite, the depositor has to give, i.e. type, the space group (example depositions: https://www.ebi.ac.uk/pdbe-xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFNAVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me why, because it is clearly a source of error. > Checking back to see the space group misparsed and re-running the water > moving-rem500 - and validation scripts would have cleared this problem with > no action needed from the depositor. I totally agree that the annotator could have intercepted the problem. But the responsibility lies with the depositor. Hooray for bureaucracy! Cheers, Robbie > > Cheers >Martyn > > > > -- > On Sat, Apr 13, 2013 23:03 BST Robbie Joosten wrote: > > >Hi Martyn, > > > >> A shame then that these 'helpful' annotators did not make use of > >> Pavel's basic sanity on the space group (*mentioned below) and check > >> back to the one listed in the uploaded PDB file. > >As far as I know, EDS is run on all new depositions at PDBe. I don't > >know whether they already did that when this model was deposited. Even > >if they did, this may not solve the problem because the PDB does not > refuse models. > >Possible scenarios (there may be more): > > > >1) Pretty bad case > >- Annotator: We cannot reproduce your R-factors in EDS. Could you check > >the annotated coordinate and reflection files? > >- Depositor: Not interested (the paper is almost accepted anyway). > >Approve model as-is. > > > >2) Worst case > >- Annotator: ... (doesn't notice the problem) > >- Depositor: ... (doesn't notice the problem) > > > >> I often wonder why the PDB does not make the deposited coordinate > >> file publicly available so that these sorts of issues can be checked > >> and > >tracked. > >Good point, I wonder about that as well. Also about whether depositors > >would like that? > > > >> The whole PDB data (excluding the EMDB that was recently merged into > >> it) amounts to about a laptop hard drive's worth of data - so surely > >> space > >can be > >> made for the deposited coordinates? (and restraint files which will > >> be > >very > >> useful for other workers including pdb-redo). > >Yes, having access to certain restraint files (particularly for LINKs) > >would be very nice. That said, a proper repository of > >consensus-restraints for hetero compounds and LINKs would be more > >reliable than potentially different restraints for each PDB entry. > > > > > Having the depositors' uploaded data would help me understand other > >> puzzling features of structures such as the current 4GRV.pdb which > >> seems > >to > >> have a list of TLS groups but contains not a single ANISOU line!... > >I'm not a big fan of using ANISOU records for TLS contributions anyway > >;-) But, more seriously, PDB entries should adhere to the PDB standard. > > > >Cheers, > >Robbie > > > > > >> > >> > >> Cheers > >> Martyn > >> > >> *In this particular case attempting to calculate R-factor using data > >> and > >model > >> files and making sure that the R you get is not twice as large as > >published one > >> would entirely suffice -:) > >> > >> Pavel > >> > >> > >> > >> From: Robbie Joosten > >> To: CCP4BB@JISCMAIL.AC.UK > >> Sent: Friday, 12 April 2013, 22:57 > >> Subject: Re: [ccp4bb] Puzzling Structure > >> > >> > >> Waters are moved during annotation using the perceived space group's > >> symmetry operation. So if the authors give the wrong space group, > >> then the annotation pipeline understandably messes things up. If the > >> originally uploaded PDB file was kept by PDBe, then the problem can > >> be recovered quite easily by the annotators. Perhaps the topic > >> starter, Michel Fodje, can > >send > >> a bug report to PDBe. In my experience, the annotators are very > >> helpful resolving these matters. > >> > >> > >> Hoping that the depositors solve the problem by themselves, is > >> probably in > >> vain: There are many crystallographers who do not read the CCP4BB > >> (which > >is > >> a shame, really); they didn't notice the enormous amount of water > >> related bumps in their final model (which is in the validation report > >> you get > >after > >> deposition and in REMARK 500 of the PDB file you have to approve); > >> they also didn't notice the huge number of symmetry-related bumps; > >> the R-factors in the PDB file are different from (and better than) > >> the ones in Table 1. > >Also > >> notice that the paper was subm
Re: [ccp4bb] Puzzling Structure
Hi Robbie, >Which seems a sort of reasonable attitude to me. > Not quite, the depositor has to give, i.e. type, the space group what I don't get is why one needs to type in this information if it is already present in both, model and data files? Any human typing is typo prone. Ideally depositor would need to provide only information that is not genuinely available in data and model files that are being deposited. > > Checking back to see the space group misparsed and re-running the water > > moving-rem500 - and validation scripts would have cleared this problem > with > > no action needed from the depositor. If original data and/or model files were not hand edited then there would not be such a problem in the first place, eliminating the need to create extra work overhead running all these great remediation tools. Pavel
Re: [ccp4bb] Puzzling Structure
Robbie Joosten wrote: Hi Martyn, I think the question is where the error was made - seeing the uploaded file would clear this up. But it seems unlikely to me that the depositor saw a huge R factor discrepancy at the end of refinement and just blithely uploaded it. So scenario 3 :- PDB : we cannot reproduce your R factor with our programs Depositor : that's your problem mate - it was fine when it left me...up to you to sort it... Which seems a sort of reasonable attitude to me. Not quite, the depositor has to give, i.e. type, the space group (example depositions: https://www.ebi.ac.uk/pdbe-xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFNAVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me why, because it is clearly a source of error. In my experience with RCSB autodep2, assuming the information was in the uploaded pdb file, this information is already pre-filled and the depositor just glances over to see it is correct. A missing or extra "(1)" might not be noticed. So perhaps it is a parsing error, perhaps related to the different ways the space group is represented on the CRYST1 card, and the different stringency of different programs in interpreting the CRYST1 card. But the validation report is included with the approval request letter, and major discrepancies are noted in the text of the validation letter in case the depositor is too busy to actually read the validation report. So if the depositor read more than the first line or two of the letter he should have known there was a problem. Then there is the 2-week default release policy: "No major issues were raised during data processing. A summary of some of the key annotations in your entry is shown below. Please verify that these are correct. If we do not hear from you within two weeks, we will consider this entry to have been approved by you. The entry will then be released according to the release/hold instructions you have provided." If this 2-week default release is the rule even when there are issues, the depositor may have put it aside to find the problem when time was available, and waited too long and let the default release kick in. eab
[ccp4bb] Angle restraints
Dear users, Validation of a structure showed a deviation in the angle between atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials of modification of the orientation failed to solve this problem. I also confirmed by deleting the side chain and refining, it confirmed the presence of complete side chain. So I proceeded to use external restraints for these two angles in refmac5 (version 5.6.0117). The keyword was as follows - external angle first chain A residue 93 atom NE next chain A residue 93 atom CZ next chain A residue 93 atom NH1 value 120.3 sigma 0.5 external angle first chain A residue 93 atom NH2 next chain A residue 93 atom CZ next chain A residue 93 atom NE value 120.3 sigma 0.5 Still there is no change in the angle, it continues to have the same deviation. So kindly suggest whether there is any error in the keyword provided or other way to handle this problem. Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Angle restraints
Hi Kavya, Which validation program did you use? How big is the deviation (in sigma values)? Is it the only outlier? What is your overall bond angle rmsZ? Using external restraints is a bit over the top here, especially if it is the only outlier. If your rmsZ is high (close to or over 1) then you may want to try tighter geometric restraints overall. In a normal distribution it is not surprising to find a 'true' outlier, so if your structure is large you need to worry less. Cheers, Robbie Sent from my Windows Phone From: Kavyashree Manjunath Sent: 2013-04-15 07:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Angle restraints Dear users, Validation of a structure showed a deviation in the angle between atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials of modification of the orientation failed to solve this problem. I also confirmed by deleting the side chain and refining, it confirmed the presence of complete side chain. So I proceeded to use external restraints for these two angles in refmac5 (version 5.6.0117). The keyword was as follows - external angle first chain A residue 93 atom NE next chain A residue 93 atom CZ next chain A residue 93 atom NH1 value 120.3 sigma 0.5 external angle first chain A residue 93 atom NH2 next chain A residue 93 atom CZ next chain A residue 93 atom NE value 120.3 sigma 0.5 Still there is no change in the angle, it continues to have the same deviation. So kindly suggest whether there is any error in the keyword provided or other way to handle this problem. Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
