Hi, I was not implying to cut-out the bad pieces and apologize if it appeared as such. In my short time in crystallography the lowest resolution I have worked with is 1.95 A. This was only an example to help-out, and appeared to be the best and complete answer to the question. Jason, I goofed in typing, you can leave out the parenthesis if you create an object.
isomesh mesh1, your map, 1.0, chainA I removed carve :) Sincerely, Carlos >>> Phoebe Rice <pr...@uchicago.edu> 05/10/09 2:22 PM >>> 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. ---- Original message ---- >Date: Sat, 9 May 2009 18:53:35 -0500 >From: Carlos Huerta <carlos.hue...@utsouthwestern.edu> >Subject: Re: [ccp4bb] Manipulating electron density >To: CCP4BB@JISCMAIL.AC.UK > >Hi Jason, > >If you already created a .map from CCP4 and changed the extension to .ccp4. Then, to create a map in PyMol for your protein only is the following. > >create chainA, (chain A & pdb name) #I think you can leave out the pdb name >isomesh mesh1, your map, 1.0, (chainA), carve=1.5 > >If the chain contains other atoms beside the protein atoms. > >create chainA, (chain A & resi #-#) >isomesh mesh1, your map, 1.0, (chainA), carve=1.5 > >Sincerely, > >Carlos > > >>>> Jason Porta <jpo...@unmc.edu> 05/09/09 3:19 PM >>> >Hi everybody, > >Sorry if this message was already asked (I could not find it in the archives). I am making a >figure of a recently solved protein structure including the electron density. I would like the >electron density to cover only the protein, and not the surrounding space where the >symmetry-related atoms are. I remember this being a simple task with Xfit, but I cannot >find a copy for Intel-based Macs. > >I have tried doing this using Coot and PyMol, but have had no luck as of yet. I have also >tried using Mapmask in CCP4, which also did not work. > >Any suggestions would be greatly appreciated. > >Jason Porta >Graduate Student >Dept. Biochemistry & Molecular Biology >University of Nebraska Medical Center >Omaha, NE 68198 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
