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
-------------------------------------------------------
This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
Tool for open source databases. Create drag-&-drop reports. Save time
by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
Download a FREE copy at http://www.intelliview.com/go/osdn_nl
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
