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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