pymol-users

[PyMOL] Electronic density maps

[Konrad H. <hi...@cn...>]

I am trying to visualize electronic densities that I prepare in my own=20=

code. This means that I have to write them in XPlor format in order to=20=

load them into PyMOL. Is there anywhere a detailed description of that=20=

format, preferably with some example files? The best I could find is a=20=

summary.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

RE: [PyMOL] Electronic density maps

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

Konrad,

There are several options for loading map data into PyMOL now:

XPLOR (format=3Dxplor)
CCP4  (format=3Dccpy)
O/BRIX (format=3Dbrix)

In addition, you can use the following non-crystallographic formats:

Delphi/Grasp PHI files (format=3Dphi)
AVS FLD files (as output from MEAD) (format=3Dfld)

and in the current CVS, we have support for DX files output by APBS
(format=3Ddx).

You can also bypass the file entirely and load an orthogonal "ChemPy =
brick"
into PyMOL via NumPy.  Example code for this can be found in
examples/devel/brick01.py.  Note that you must use a PyMOL build that
included numeric Python in order for this to work (the RPMs and Linux
binaries do not have it, so you may need to build from source using the
_PYMOL_NUMPY define).  There's also a "ChemPy Map" approach, which =
expects
opaque packed C float data.

Once in PyMOL, you can then use "isomesh" and "isosurface" to create =
mesh
and solid isocontours.  Or use "ramp_new" and=20
"color" to color by the potential found in the map.

Sorry about the lack of documentation -- it will improve.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Konrad Hinsen
> Sent: Monday, June 21, 2004 7:10 AM
> To: <pym...@li...>=20
> <pym...@li...>
> Subject: [PyMOL] Electronic density maps
>=20
> I am trying to visualize electronic densities that I prepare=20
> in my own code. This means that I have to write them in XPlor=20
> format in order to load them into PyMOL. Is there anywhere a=20
> detailed description of that format, preferably with some=20
> example files? The best I could find is a summary.
>=20
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
> ---------------------------------------------------------------------
>=20
>=20
>=20
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Re: [PyMOL] Electronic density maps

[Konrad H. <hi...@cn...>]

On Jun 21, 2004, at 17:36, Warren DeLano wrote:

> Konrad,
>
> There are several options for loading map data into PyMOL now:
>
> XPLOR (format=xplor)
> CCP4  (format=ccpy)
> O/BRIX (format=brix)

Good to know! At least the CCP4 one is documented, but being a binary 
format, it's a bit of a pain to use.

> You can also bypass the file entirely and load an orthogonal "ChemPy 
> brick"
> into PyMOL via NumPy.  Example code for this can be found in

That sounds a lot better!

> examples/devel/brick01.py.  Note that you must use a PyMOL build that
> included numeric Python in order for this to work (the RPMs and Linux
> binaries do not have it, so you may need to build from source using the
> _PYMOL_NUMPY define).  There's also a "ChemPy Map" approach, which 
> expects
> opaque packed C float data.

Well... My choice is PyMOL 0.86 under Linux with NumPy (but 0.86 
doesn't seem to have the ChemPy Brick stuff yet), or 0.95 under MacOS 
(the hybrid build, without NumPy). So I am out of luck... and I can't 
mess around with installations at the moment.

I'll see if I can get CCP4 format to work in a reasonable amount of 
time...

<rant>
Why can't the crystallography community agree on one file format and 
document it properly?
</rant>

Konrad.

Re: [PyMOL] Electronic density maps

[Konrad H. <hi...@cn...>]

On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:

> I'll see if I can get CCP4 format to work in a reasonable amount of=20
> time...

Actually I went for XPlor in the end, after getting a useful hint:

	http://cns.csb.yale.edu/v1.1/tutorial/text.html

Problem: the XPlor format does not specify the absolute position of the=20=

map in space. PyMOL must choose it somehow. Unfortunately, it makes the=20=

choice in such a way that my protein (in a PDB file) is outside the=20
map.

Is it possible to shift the map (by a numerically specified distance)=20
after it has been loaded? I'd rather shift the single map than redoing=20=

a few dozen PDB files.

Konrad
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

RE: [PyMOL] Electronic density maps

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

Konrad,

	Using crystallographic formats like XPLOR for generic volume
visualization is tricky because ultimately the map must be aligned on a =
grid
which passes through the origin.  In other words, the grid spacing must
include the origin even if the map itself does not.  In order to shift =
the
map away from the origin, you need to move the interval away from the
origin.

For example, to get a map covering the interval 25 to 75 along an axis =
in
XPLOR format, you would need to provide the information as follows:

There unit cell axis is 50 Angstroms.
There are 50 divisions per unit cell.
The range for this axis is 25 to 75.

etc.

Cheers,
Warren



--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Konrad Hinsen
> Sent: Tuesday, June 22, 2004 3:58 AM
> To: <pym...@li...>=20
> <pym...@li...>
> Subject: Re: [PyMOL] Electronic density maps
>=20
> On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:
>=20
> > I'll see if I can get CCP4 format to work in a reasonable amount of=20
> > time...
>=20
> Actually I went for XPlor in the end, after getting a useful hint:
>=20
> 	http://cns.csb.yale.edu/v1.1/tutorial/text.html
>=20
> Problem: the XPlor format does not specify the absolute=20
> position of the map in space. PyMOL must choose it somehow.=20
> Unfortunately, it makes the choice in such a way that my=20
> protein (in a PDB file) is outside the map.
>=20
> Is it possible to shift the map (by a numerically specified=20
> distance) after it has been loaded? I'd rather shift the=20
> single map than redoing a few dozen PDB files.
>=20
> Konrad
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
> ---------------------------------------------------------------------
>=20
>=20
>=20
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>=20