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On Thu, 7 Sep 2006, Mark J. van Raaij wrote:
> probably the more "scientifically honest", informative way to do it
> (minimising model bias) would be to show a difference density map
> with the ligand omitted from the model with the model refined
> omitting ligand. Then you would have no, or very little other density
> than the one for the ligand.
> Mark
>
> On 7 Sep 2006, at 16:05, Fred. Vellieux wrote:
>
> > Hello there,
> >
> > The way I am doing it: I use Turbo-Frodo, the plot option produces a
> > PostScript file (I don't know if PyMOL does produce a PS file).
> >
> > Then I import into Illustrator and select and remove the vectors I
> > don't
> > need. Fastidious but works pretty well...
> >
> > Fred.
I already mentioned this in private to Tassos: I work with a box. That
encloses the ligand, cofactor, whatever. Plus of course the rest (solvent,
protein...)
There is often some density in the front or in the back that messes up the
picture. I want to remove that. However, should the density of my
cofactor, ligand... be connected to density for solvent, or density
corresponding to a side chain then any attempt to fudge that by removing
vectors would be noticed... like a hole appearing in the density for the
object.
So removing such vectors (density vectors appearing in the back or in the
front with Illustrator) is fine, if I happen to remove one vector I did
not want then there's the command to undo the last delete operation.
And more importantly if I try to mess up the density of the object I want
to show (such as, for low resolution reasons, a connection to density
corresponding to water) it will be noticeable. Pretty good reason not to
attempt to cheat if you know it's visible...
Fred.
--
s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0) 438785494
e-mail: [EMAIL PROTECTED]
