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.
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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