I'd support BR's position. Why the compelling urge to fill every blob with atoms? Density should only be modeled when its interpretable. One can comment about the blob in a paper, and perhaps even show maps for the region, indicating that there might be something there if its believed to be a functionally important region. One could deposit without building in this site, but say that combinations of disorder ions/water etc all fit the density equally well. ________________________________________ From: Bostjan Kobe [b.k...@uq.edu.au] Sent: Wednesday, February 03, 2010 8:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unknown density
I think there is at least one more option here (relevant at least in some rare cases): Identifying what that something is likely to be can be significant and may advance your career Of course it is important to present supporting or otherwise evidence for the interpretation. As already discussed, this is difficult in a PDB file, and that’s why the accompanying publication can be very important. Bostjan On 4/02/10 3:54 AM, "Bernhard Rupp" <b...@ruppweb.org> wrote: General remark – if I may Putting nothing in: no significant effect on model and life in general Putting ‘something’ potentially wrong and misleading in: could be detrimental to your career BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Katja Schleider Sent: Wednesday, February 03, 2010 9:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unknown density Dear all, I found some fairly substantial density in the active site of my protein structure. But I don´t know what it should be. My crystallisation condition consists of lithium sulfate, citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit of sense! Any suggestions to fill this density with something? Picture is attached. Thanks a lot, Katja __________________________________________________ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
