Yeah that's perfect. Just what I was looking for!
One other thing, anyone know how to turn the stereo visual off
completely so that pymol doesn't load into an opengl stereo visual even
if pymol detects that you have stereo capable hardware? Even when stereo
is turned off the screen flickers like its in stereo mode. Is there some
kind of pymol startup switch or environment variable to disable loading
into a stereo window?
Michael George Lerner wrote:
Hi,
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Mr. Lerner,
Thanks for letting me know about the PDB2PQR server. I was able to
generate a pqr from the NBCR website that then works with APBS to
generate the dx map.
I'm not sure how to get the same electrostatic gradient effect on the
molecule surface generated using APBS tools using the isosurface
command. I really like the potential mapping to molecular surface
visual and it would be nice if it could be done with more than one
molecule (from separate pdb files). I guess I can just render one
molecule at a time and then crop multiple images into a single
document so it looks like one system.
Oops .. my fault. I was reading quickly, and I thought you wanted
different isosurfaces for each molecule, not different molecular
surfaces. The APBS plugin can't handle what you want, but you can do
it. You need to load a map and a molecule, create a ramp that controls
the coloring and attach that ramp to the molecule's surface. Here's an
example (assuming you have pdb files firstmol.pdb and secondmol.pdb and
dx maps firstmap.dx and secondmap.dx):
-- begin --
# load the molecules and maps
load firstmol.pdb
load firstmap.dx
load secondmol.pdb
load secondmap.dx
# create the ramps and show the surfaces
ramp_new firstramp, firstmap, [-10,0,10]
set surface_color, firstramp, firstmol
show surface, firstmol
ramp_new secondramp, secondmap, [-10,0,10]
set surface_color, secondramp, secondmol
show surface, secondmol
--- end ---
This is kind of ugly, though: it creates both of the ramps in the same
place, and i don't know how to move them. So, if you want to change the
scales, you probably need to delete the ramp and give a new set of
ramp_new, set and show commands.
Does that help?
Question: do people want the APBS plugin to support multiple molecules?
I can probably put something in, but it would take a bit of work (and
I'll have to think about how to keep the interface small enough for
"normal" screen sizes).
-michael
Thank you very much,
Sabuj Pattanayek
Michael George Lerner wrote:
Hi,
I've been meaning to update APBS tools so that some of the warnings
are larger and better explained.
WARNING: 53 atoms did not have properties assigned
means that PyMOL couldn't automatically assign properties for 53
atoms in yoru molecule. This is usually because you have
non-standard protein residues (or because you're not using a protein
at all). In this case, you'll need to teach PyMOL about your
molecule (via chempy .. it's a little involved. I think Warren
posted something about it recently) or use another program to
generate the PQR file.
If you can get a good PQR file from another source (e.g. there's an
APBS web portal at https://gridport.npaci.edu/apbs/ that probably
understands more molecules than PyMOL), then you can use APBS tools
directly with that PQR file.
For your second question, you'll have to have to make the surfaces
yourself, as the APBS Plugin only supports one molecule/map at a time
right now. Have you looked at the help information for isosurface?
You may also have to create two different dx maps and load them in by
hand so that they have different names. You can use the
'Configuration' pane of the APBS plugin to make sure that they get
reasonable names when you create them (then you just use PyMOL's load
command to load them).
Is that enough to get you started?
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Pymol users,
I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first
clicking the Set grid button, then clicking run APBS, but I get the
error message shown below.
coarsedim is [119.03399429321288, 109.91349792480469,
143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.4549999237060547]
finegridpoints is [193, 193, 225]
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
WARNING: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!
Another problem I've come across when trying to load phi maps
exported from Grasp is described below:
1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with
molecule x, set values for say -16kt/e, 0, 16 kt/e, and show the
surface, this looks as it should.
4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize, set phi map y to correlate with
molecule y, set values for say -16kt/e, 0, 16 kt/e, and show the
surface, this looks as it should for pdb y but the remaining
isosurface from phi map y gets mapped onto pdb x and the x surface
no longer looks like it should.
..so is there anyway to load two phi maps and map them to the
surfaces of their correlating molecules without exceeeding their
respective surface boundaries?
Thanks,
Sabuj Pattanayek
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