Dear Hussain,
in the electron density example of this tutorial, the parameter
"carve=1.6" is used, which means that density is only shown within a
radius of 1.6 A around atoms. This is usually done for clarity, but may
give an unrealistic impression of the density quality. Here, you should
carefully choose a radius that shows the density similar as in a plot
without any "carve" parameter, while cutting away the density from the
surrounding atoms that you don't want to show. I've made good
experiences choosing a radius similar to the maximum resolution of your
data as a starting point. The "carve"-radius should then be reported in
the figure.
Good luck,
Dirk.
Am 13.04.10 15:40, schrieb Ed Pozharski:
Hussain,
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html
which is the top hit when you google "pymol electron density". Using
google (and not to appear biased, other available search engines) is the
most valuable advice (per word) that you may possible get.
On Tue, 2010-04-13 at 18:33 +0530, Hussain Bhukyagps wrote:
Dear all,
How can i show electron density map for my ligand in pymol, which is
bound in the active site.
i uploaded map as .xplor extension to the map file..
thank u
Hussain
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