Dear all,
I made a PQR file by PDB2PQR, and then in PyMOL, I run apbs.
I got an error. Help.
PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
A current PyMOL Maintenance and/or Support Subscription may be required
for legal use of this Build beyond a finite honor-system evaluation
period.
Please visit http://www.pymol.org/funding.html for more information.
This PyMOL Executable Build incorporates Open-Source PyMOL 0.99beta37.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: Quadro4 750 XGL/AGP/SSE2
GL_VERSION: 1.5.2 NVIDIA 66.29
Adapting to Quadro hardware.
Detected 2 CPUs. Enabled multithreaded rendering.
CmdLoad: "pdb3929-out" loaded as "pdb3929-out".
APBS Tools: set pqr file to
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr
cs [5, 7, 8]
finedim [71.384999990463257, 96.904001235961914, 116.09099578857422]
nlev 4
mult_fac 32
finegridpoints [161, 225, 257]
Maximum number of grid points exceeded. Old grid dimensions were [161,
225, 257]
Fine grid points rounded down from [81, 113, 129]
New grid dimensions are [65, 97, 129]
APBS Tools: coarse grid: (87.354,130.737,163.355)
APBS Tools: fine grid: (71.385,96.904,116.091)
APBS Tools: center: (-22.203,10.832,100.751)
APBS Tools: fine grid points (65,97,129)
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.4.0
Nathan A. Baker (ba...@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2005. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA
----------------------------------------------------------------------
APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation
numerically. FEtk and PMG are developed and maintained by the Holst
Research Group at UC San Diego. PMG is designed to solve the
nonlinear
Poisson-Boltzmann equation and similar problems with linear space and
time complexity through the use of box methods, inexact Newton
methods,
and algebraic multilevel methods. FEtk is designed to solve general
coupled systems of nonlinear partial differential equations accurately
and efficiently using adaptive multilevel finite element methods,
inexact Newton methods, and algebraic multilevel methods. More
information about PMG and FEtk may be found at <http://www.FEtk.ORG>.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics
of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Feb 28 2006 at 10:10:21
Parsing input file pymol-generated.in...
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr.
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Problem opening virtual socket
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr!
Error reading molecules!
ObjectMapLoadDXFile-Error: Unable to open file!
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Today's Topics:
1. running macpymol in the background from the terminal (Andrew Wollacott)
2. label positions, centered, left, or right (Seth Harris)
3. RE: label positions, centered, left, or right (Warren DeLano)
--__--__--
Message: 1
Date: Wed, 22 Feb 2006 21:26:29 -0800
From: "Andrew Wollacott" <senyord...@gmail.com>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] running macpymol in the background from the terminal
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hello,
I'm running MacPyMol 0.99. I typically open pymol from the terminal (
terminal.app) using the "open" command.
open test.pdb
I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
open when I do this. The problem I have when doing this is that when
entering the "pwd" command into pymol, I get the following:
PyMOL> pwd
/
so pymol thinks it's running from the root directory. This makes it tough
for me to load more pdbfiles into pymol using the "load" command as I must
first "cd" into the directory with pymol. Just a note, that in version 0.9=
8,
using the "open" command, pymol would recognize what directory it was opene=
d
from.
Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
gets the output from pymol. I've tried to run pymol in the background so
that I can continue to use this terminal window while stilll having pymol
open. Using "pymol test.pdb &" I still get pymol output to the terminal. =
I
could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
verbose compared to "open test.pdb"
I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
t
since version 0.98 worked fine, I was wondering if anyone has a workaround
for this inconvenience.
Thanks.
- Andrew Wollacott
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hello,<br><br>I'm running MacPyMol 0.99. I typically open pymol from =
the terminal (terminal.app) using the "open" command.<br><br>>=
open test.pdb<br><br>I have .pdb files set to open with MacPyMol, so graph=
icConverter doesn't open when I do this. The problem I have when doin=
g this is that when entering the "pwd" command into pymol, I get =
the following:
<br><br>PyMOL> pwd<br>/<br><br>so pymol thinks it's running from the roo=
t directory. This makes it tough for me to load more pdbfiles into py=
mol using the "load" command as I must first "cd" into =
the directory with pymol. Just a note, that in version=20
0.98, using the "open" command, pymol would recognize what direct=
ory it was opened from.<br><br>Now, I can use the "pymol test.pdb"=
; to open pdbfiles, but then the terminal gets the output from pymol. =
I've tried to run pymol in the background so that I can continue to use th=
is terminal window while stilll having pymol open. Using "pymol=
=20
test.pdb &" I still get pymol output to the terminal. I coul=
d use "pymol test.pdb >& /dev/null &" but that seems q=
uite a bit more verbose compared to "open test.pdb"<br><br>I gues=
s I could alias pymol to essentially pipe it's output to /dev/null but sinc=
e version=20
0.98 worked fine, I was wondering if anyone has a workaround for this incon=
venience.<br><br>Thanks.<br><br>- Andrew Wollacott<br><br><br>
------=_Part_19022_27230051.1140672389773--
--__--__--
Message: 2
Date: Thu, 23 Feb 2006 10:39:32 -0800
From: "Seth Harris" <set...@gmail.com>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] label positions, centered, left, or right
------=_Part_8191_17923195.1140719972653
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Hi all,
Minor thing, but thought I'd ask...
Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom (left-anchored)=
.
Is there a way to choose whether the label is left-anchored, centered, or
right-anchored?
I find that it's hard to offset the label sufficiently with commands like:
label myprot and name ca, " %s%s" % (resn,resi)
which used to get the label to float nicely just to the right of the atom.
Now that the label is centered the spaces don't help push the labels over a=
s
much as they used to, and the obvious route of adding twice as many spaces
somehow isn't getting me there. I thought there might be an anchor, align,
or justification flag on the labels.
I did also notice that in editing mode you can drag the labels to whatever
position you wanted in recent betas. Very nice!
Cheers,
Seth
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Hi all,<br>
<br>
Minor thing, but thought I'd ask...<br>
<br>
Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom
(left-anchored). Is there a way to choose whether the label is
left-anchored, centered, or right-anchored? <br>
<br>
I find that it's hard to offset the label sufficiently with commands like:<=
br>
<br>
label myprot and name ca, " %s%s" % (resn,resi)=
<br>
<br>
which used to get the label to float nicely just to the right of the atom. =
<br>
Now that the label is centered the spaces don't help push the labels
over as much as they used to, and the obvious route of adding twice as
many spaces somehow isn't getting me there. I thought there might be an
anchor, align, or justification flag on the labels. <br>
<br>
I did also notice that in editing mode you can drag the labels to whatever =
position you wanted in recent betas. Very nice!<br>
<br>
Cheers,<br>
Seth<br>
------=_Part_8191_17923195.1140719972653--
--__--__--
Message: 3
Subject: RE: [PyMOL] label positions, centered, left, or right
Date: Thu, 23 Feb 2006 10:53:21 -0800
From: "Warren DeLano" <war...@delsci.com>
To: "Seth Harris" <set...@gmail.com>,
<pymol-users@lists.sourceforge.net>
Seth,
Yes, via the "label_position" setting which specifies x,y, and z
alignment of labels.
Values in the range [-1,1] imply alignment. Beyond that, it is a
translation along camera axes in model-space dimensions. =20
# for left alignment 0.75 A in front of atom
set label_position, [-1,0,1.75]
# for right alignment directly on atom
set label_position, [1,0,0]
# for left alignment 1 A to right of atom
set label_position, [2,0,0]
# for center alignment 2 A below atom
set label_position, [0,-3,0]
# centered 3 A in front of atom
set label_position, [0,0,4]
etc.
Cheers,
Waren
--
Warren L. DeLano, Ph.D. =20
Principal Scientist
. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213 =20
. South San Francisco, CA 94080 USA =20
. Biz:(650)-872-0942 Tech:(650)-872-0834 =20
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com =20
=20
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net=20
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of=20
Seth Harris
Sent: Thursday, February 23, 2006 10:45 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] label positions, centered, left, or right
=20
Hi all,
=20
Minor thing, but thought I'd ask...
=20
Labels now appear to be centered on whatever atom they are=20
labeling. Previously, the left-hand side of the label was on=20
the atom (left-anchored). Is there a way to choose whether=20
the label is left-anchored, centered, or right-anchored?=20
=20
I find that it's hard to offset the label sufficiently with=20
commands like:
=20
label myprot and name ca, " %s%s" % (resn,resi)
=20
which used to get the label to float nicely just to the right=20
of the atom.=20
Now that the label is centered the spaces don't help push the=20
labels over as much as they used to, and the obvious route of=20
adding twice as many spaces somehow isn't getting me there. I=20
thought there might be an anchor, align, or justification=20
flag on the labels.=20
=20
I did also notice that in editing mode you can drag the=20
labels to whatever position you wanted in recent betas. Very nice!
=20
Cheers,
Seth
=20
=20
--__--__--
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