If one limits such a comment system to authors of PDB structures then you are closing the door to a lot of potentially good contributors: anyone involved in analysing protein structures. For instance that can be anyone in the fields of structural bioinformatics, molecular dynamics, computational crystallography etc. Those people can have quite a say in these discussions and are even very likely to find issues since they write tools to automatically analyse PDB structures.
As I said, I'd go for a system totally open for anyone who wants to register. Modern tools to allow scoring of the feedback by the rest of the community would sort all problems out, provided there is enough participation. Jose -----Original Message----- From: CCP4 bulletin board on behalf of Zachary Wood Sent: Thu 5/15/2014 7:41 PM To: [email protected] Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone I agree with Nat. If you think a structure has a problem area, it is much easier to point it out to the users than to publish a rebuttal. Comments are easy. Simply state your observation. If you are wrong in your assessment, I am sure you will receive a fine education from the more learned individuals in our community. And since this pertains to the entire PDB, I do not see a lot spam/noise being produced on a single structure. I would suspect almost nothing will be said regarding the majority of the 100,000 structures. I am not aware of a ton of spam being produced on the publications in the Pubmed Commons. In fact, it saddens me that no one has said anything significant about my publications. I personally would prefer to limit the feedback to those who deposit structures (similar to how Pubmed Commons limits comments to authors). I believe that we as a community are the ones best positioned to police the database. Best regards, Z *********************************************** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** Best regards, Z *********************************************** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** On May 15, 2014, at 1:00 PM, Nat Echols <[email protected]> wrote: > On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart <[email protected]> > wrote: > It seems to me that the Wikipedia mechanism works wonderfully well. One rule > is that you can't make assertions yourself, only report pre-existing material > that is attributable to a "reliable published source". > > This rule would be a little problematic for annotating the PDB. It requires > a significant amount of effort to publish a peer-reviewed article or even > just a letter to the editor, and none of us are being paid to write rebuttals > to dodgy structures. > > -Nat
