This is not such a problem when using the old "Map-cover" command
in O, because the cut-offs are flat planes, you would get cubic
density around each atom which would raise the suspicion of even
the most gullible reader.
But a better solution would be to not contour the carved surface-
leave a gaping hole in the net where something else is connected.
Another way to describe this-
contour the real density, but only display the contours within
certain radius of selected atoms. Then in Anastassis's example
there would be no density for the atoms because the contour is
outside the cutoff.
Anastassis Perrakis wrote:
Dear Andrew,
Thank you for that posting; I would like to simply agree with the
Bobscript manual and your suggested practice.
I think the 'carve' commands should not be there; if you wonder why,
take a ligand, put it wherever you want in space,
set the map sigma to -0.5, display a map with carve=1.2 and think if
this picture is informative, especially in the context
of your favorite competitor publishing it in Nature.
A.
PS Yanming, if you really want to do that what you ask for, ADOBE
ILLUSTRATOR IS THE BEST WAY TO GO
*From: * [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
*Subject: * *Re: [ccp4bb] pymol help*
*Date: * October 29, 2007 8:44:46 GMT+01:00
*To: * CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Reply-To: * [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
Dear all,
Sorry I did not make it clear in my first email. Now my question can
boil down to:
IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS
UN-ZOOMED IN PYMOL?
thanks
Yanming
On Oct 29, 2007, at 13:43, Andrew Gulick wrote:
I'd be curious to know if there is any consensus in the community with
using
the "carve" command for showing maps. I have never felt comfortable
showing
density within a cutoff radius of a particular residue or--even worse--a
ligand, and felt the figures should display the extraneous bits as well.
The burden was on the crystallographer to find an appropriate view (slab,
sigma, etc...) to display the map.
The Bobscript manual appears to agree with me on this one as it states:
http://www.strubi.ox.ac.uk/bobscript/doc24.html
"If your density is good then you will just have density over residue 999,
but if things are not so hot then you may want to cheat and just draw the
bits of density near to the selected atoms."
Just curious,
Andy
--
Andrew M. Gulick, Ph.D.
-----------------------------------
(716) 898-8619
Hauptman-Woodward Institute
700 Ellicott St
Buffalo, NY 14203
-----------------------------------
Senior Research Scientist
Hauptman-Woodward Institute
Assistant Professor
Dept. of Structural Biology, SUNY at Buffalo
http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html
http://labs.hwi.buffalo.edu/gulick
On 10/29/07 4:40 AM, "Stefan Schmelz" <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Dear Yanming,
To show "pretty" density of a model you have to import a ccp4 density
map and display it around your ligand. The simplest solution is using
ccp4 and tick the box "Generate weighted difference maps files in CCP4
format" when running Refmac5 (one or two cycles are enough). Specify
names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4.
This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density
around our ligand you can use the following command:
isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8
("map" = greats an object name map, "name_of_fwtmap" = name of your map,
"1.0" = Sigma level, "carve=1.8" = width map is displayed around your
ligand
This will allow you to show a "pretty" electron density map around your
ligand without any chemical info of the ligand.
Stefan Schmelz
Yanming Zhang wrote:
Hi, all,
I want to make a pymol figure wich can show the pretty density of a
ligand. But we don't want to show the detailed chemical info of the
ligand. If I use a large enough sphere_scale for the ligand, the
chemical info will be hidden but the density map will be disrupted. If
I use a smaller sphere_scale, the density looks great but the chemical
info of the ligand will be visible. How should I overcome this dilemma?
Thank you very much for your help.
Yanming
