You're right; my apologies to the original question-poster. I think a better way to do it would be with a mask that covers the entire molecule of interest, rather than an atom-by-atom carving job.
Phoebe ---- Original message ---- >Date: Sun, 10 May 2009 20:29:00 -0700 >From: James Stroud <xtald...@gmail.com> >Subject: Re: [ccp4bb] Manipulating electron density >To: CCP4BB@JISCMAIL.AC.UK > >On May 10, 2009, at 12:21 PM, Phoebe Rice wrote: >> Of COURSE the map will look lovely if you carve it off at 1.5A >> from your atoms. And your gels will look lovely too if you >> just touch them up with with some white-out and a sharpie. >> Do the honest thing and show the whole truth, using the >> z-clipping to get a comprehensible slab. > >Maybe we should give Jason the benefit of the doubt that he wants to >present an honest representation of his density. Clipping off symmetry >related molecules is not the same as "carving" density from amorphous >blobs. The former is more akin to showing only part of a lane of a >gel, which is common practice even in prestigious journals. In fact, >my other monitor presently displays such a "carved" gel picture from a >recent Cell paper. > >James Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
