RE: [PyMOL] RE: EMizing an xray structure (Warren DeLano)

[Warren D. <wa...@de...>]

Sarina,

I'm not sure where that "3D10" is coming from -- it should simply be the
number 10:

alter all, b=3D10

map_new can take a selection as its fourth argument, so you could
generate an independent map for each subunit, show the surface, and
color it independently.  It's also possible to color a surface by atomic
proximity, but the approach is a bit convoluted:

load some.pdb, prot
util.cbc prot
alter prot,b=3D10
set gaussian_resolution, 9.0
map_new dcalc, gaussian, 3.0
map_double dcalc
isosurface dsurf, dcalc, 1.0, prot
ramp_new dramp, prot, [-10,0,10]
color dramp, dsurf


Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
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. DeLano Scientific LLC =20
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. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
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. mailto:wa...@de...     =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sarina Bromberg
> Sent: Thursday, December 01, 2005 9:45 AM
> To: pym...@li...
> Subject: [PyMOL] RE: EMizing an xray structure (Warren DeLano)
>=20
> Warren,
> These commands (see below) go a long way toward solving the=20
> problem of producing low resolution simple structures for my=20
> textbook project. I have some questions:
>=20
> The first command elicits an error:
> PyMOL>alter all,b=3D3D10
> Alter-Error: Aborting on error. Assignment may be incomplete.
>    File "<string>", line 1
>      b=3D3D10
>          ^
> SyntaxError: unexpected EOF while parsing
> Alter-Error: Aborting on error. Assignment may be incomplete.
> Alter: modified 0 atoms.
>=20
> The rest work fine.  For a multimeric protein, how do I get=20
> different surface colors on different chains?  I tried=20
> selecting the chains and coloring them differently before=20
> running the commands below, but the dsurf object was just one=20
> color.  Can I make each chain a different object and add ",=20
> objectname" to each of these commands?
>=20
> Thanks!
> Sarina
>=20
> > Message: 6
> > Subject: RE: [PyMOL] EMizing an xray structure
> > Date: Wed, 30 Nov 2005 16:51:07 -0800
> > From: "Warren DeLano" <wa...@de...>
> > To: =3D?iso-8859-1?Q?Andreas_F=3DF6rster?=3D =
<an...@bi...>,
> > 	<pym...@li...>
> >
> >
> > Try a command sequence like this:
> >
> > alter all,b=3D3D10
> > set gaussian_resolution, 9.0
> > map_new dcalc, gaussian, 3.0
> > map_double dcalc
> > isosurface dsurf, dcalc, 1.0
> >
> > Cheers,
> > Warren
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