Hi everyone,
I am trying to run apbs from pymol (0.98) on window and always end up
getting following error message.
objectMap load DX file-error: unable to open file!
Even after using improved plugin apbs tools.py , same error message.I
also tried using externally generated .PQR file as an
I have the same problem on a mac G5 dual processor with newly compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
Interestingly, the programs work fine together on my mac G4 laptop, with
single
Sorry Viktor and Warren, but I don't think your suggestions are
applicable. I have only a single protein molecule in my trajectory,
which I kept centered at the origin, so it never traverses the
periodic boundary. I did strip all but 20 waters from it using ptraj
and created the
Hi,
I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server.
I started doing some modeling after about 6 months hiatus.
I'm using MacPymol 0.99b29 (no flickering with this).
But
it's slower than molasses. I get:
Ray: total time: 16.16 sec. = 222.8 frames/hour (32.15 sec. accum.).
This is
Default view, white with black background (sticks):
Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.)
Surface ray (white w/ black background):
Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.)
About the times I've been seeing for equivalent work I've been
Michele,
Did you just migrate from an older version? We switched PyMOL over to
perspective-based rendering (WYSIWYG with OpenGL) as the default at some
point in the past year. You can still render orthoscopically if you'd
prefer:
load 1alk.pdb
show surface
set orthoscopic
set hash_max=160
ray
My question is: how to save multiple objects from pymol as one nice pdb
file, for instance with each object with different chain name?
alter SymgenObject,chain 'X'
and repeat as needed for all objects (changing the chain as needed). Then
use all of your objects as the selection for save (aka
Stuart,
Stuart Endo-Streeter stuart.endostree...@duke.edu
Default view, white with black background (sticks):
Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.)
Surface ray (white w/ black background):
Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.)
I have the same problem on a mac G5 dual processor with newly
compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
Interestingly, the programs work fine together on my mac G4 laptop,
with
Hi folks,
Sorry for the slightly of topic question but I figure you guys know
whats going on.
I have a linux box with RHE WS 4 and I have just installed the nvidia
driver (7676 x86) which at least works so far! The problem is that the
screen will occasionally (and randomly) start flickering
Any body know how to fix this. Have people tested this driver? Should I load
an earlier driver?
When dealing with NVidia cards, I've found this is always the first thing
to try whenever a problem arises. Their Linux drivers are updated to
support new hardware and fix old bugs, but they often
I'm trying to make a high-quality figure showing ligand binding in a
cleft, incorporating sticks, electron density, and some combination of
cartoon/surface/lines for the protein. Ray-traced shadows make the
perspective much clearer but also add visual noise - for instance, the
electron
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