Thanks to all of those that sent in their comments. For those that have an interest in the consensus (after ~24 hours): For question one about the PDB deposition code- out of 10: 3 said in footnote, 2 said they had either seen or had put the deposition code in the materials and methods, and a majority indicated that it shouldn't matter, but from a pragmatic standpoint the "editor is always right" or "house rules". There is no indication in the notes to authors for this journal, which would have been the obvious way to find out where this information should go. It was also pointed out that the IUCr journals helpfully put this on the front page, so again it shouldn't matter where it is in the text. For question two on the 'rotamer-quality score' from MolProbity- 6 guessed that what was meant was the number associated with poor rotamers (i.e. in this case 12) and possibly the percentage (2.3%), but no one was actually sure that this was the case. So although I guessed incorrectly, at least it was a bit of a sanity check for me, as I hate to miss the obvious. I also got some helpful hints as to how to improve this number. I'll go with the consensus and see whether I get another berating or relief at getting it correct. Thanks again to everyone for their comments. Cheers, tom
From: Peat, Tom (CMSE, Parkville) Sent: Thursday, 17 October 2013 1:59 PM To: 'ccp4bb@jiscmail.ac.uk' Subject: questions Dear CCP4 community, I would like to tap into the collective wisdom of you folks on two questions, both of which have put me into the bad graces of a particular editor. The first question seems trivial, but I will ask it anyway- where would you put the PDB deposition code in a manuscript? I may be old fashioned, but I have put it in the footnotes just prior to the references (which also ends up being the acknowledgments section in some journals), into Table 1 or in some more chemistry oriented journals in the footnotes on the first page (often near the author information). I've been told that it obviously goes into the Materials and Methods section (where I cannot ever remember seeing it, but my memory seems to be fading with old age). I find this a little strange as I consider the final model to be a result and not a material used to produce data nor a method. But maybe people are now putting their results into the methods section. So opinions on this question are welcome. The second question is hopefully straight-forward. I was also asked to put a number in Table 1 which I am happy to do, but I don't understand how to get this number. I was asked to put the 'rotamer-quality score' from MolProbity into the table. I don't run MolProbity often, but the output I got from the server doesn't have a 'rotamer-quality score' that I can find (see attachment). Is there some option that I am missing that gives this elusive factor? I also took a look at the Chen et al paper (Acta Cryst D, 2010) on MolProbity and it mentions a rotamer-quality score for specific residues but doesn't refer to an overall score (which is what I am assuming is needed for a table). I already have the well known Ramachandran percentages (favourable, allowed /poor and outliers) in the table, so the editor clearly wants something different. When I took a guess by putting in the 'MolProbity score' I was basically called an idiot that can't follow directions. Help on this front would be appreciated as although I have been called worse things, it would be nice to eventually get what is being referred to. Thanks, tom Tom Peat CSIRO, Melbourne, Australia
