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 <[log in to unmask]>
>Subject: Re: [ccp4bb] Manipulating electron density
>To: [log in to unmask]
>
>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 <[log in to unmask]> 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
|