Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to
use an externally generated pqr file. The current mechanism for calling
pdb2pqr from within the APBS Tool results in pdb2pqr running under the same
python as pymol.
Jack
On Mon, Dec 2, 2019 at 5:58 PM Jack Ho
You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff
and
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff
applied over Pmw_2_0_0.
Jack
FYI, the reason that the ubuntu pymol 2.1.0 package currently doesn't
use the PyQT interface in the presence of the libqt5opengl5 package is that
they are hard coding pymol to use pmg_tk with the patch...
$ cat 50_force_tk.patch
Description: Disable the Qt interface to ensure the Tk interface i
O3POP-0.86000 2
C C 0.380 3
O O -0.380 3
Of course this is with some of the protons deleted from the -ignh flag
in pdb2gmx.
Thanks in advance for any advice on how to be handle this issue.
Jack Howarth
Richard,
Actually I don't have a copy of Delphi available (hence the use
of APBS). I did notice that I see more positive surface area on a
molecule with a -13 net charge when the run is done with pdie of 2.0
compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also
noticed an oddity
I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map i
Has anyone noticed major differences between the results obtained in
GRASP when using the method...
1) Read| PDB file
2) Read|Radius Charge File(+Assign)
Input AMBER.crg
3) Build|Molecular Surface|All atoms
4) Calculate|New Potentail Map
5) Calculate|Pot. via Map at Surfaces/Atoms|All atoms
Daniel,
Did you use the 'glxinfo' command in an xterminal under FC2
to check if 'direct rendering: Yes' is reported. Assuming you
have your board in an AGP slot and used the System Settings->
Display control panel to enable the radeon driver, the resulting
xorg.conf should be preconfigured to e
Has anyone successfully built pymol 0.95 under Fedora Core 2?
Are there any particular tricks? My first attempt of just editing
Rules.make to change python2.2 to python2.3 allowed the compilation
to finish but I get the following run-time error...
Exception in thread Thread-1:
Traceback (most r
What exactly is the recommended approach for installing
and maintaining custom pymol python scripts? While I have seen
messages describing custom pymol scripts, their installation isn't
described. Should I put them in the python directory tree or in
the pymol directory tree with the rest of p
Is there any chance we can get pymol 0.9 moved over from
unstable to stable for the 10.2-gcc3.3 release?
Jack
Is anyone here seeing problems running pymol 0.86 on a recent
Irix (6.5.17 or 6.5.18)? I am seeing some odd things here on several
machines. One of machine with 6.5.18 runs the prebuilt pymol 0.86 fine.
The other two with the same Irix have problems. I get random freezes
in pymol either as the
Under linux does anyone else see the following? If one
loads in the 1pit.pdb from the MOLMOL data files, the
resulting structure seems to have extra bonds drawn in the
side chains. For example phe's seem to have all the opposing
carbons in the rings interconnected through the center of
the ring
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