thanks a lot for reply.
Problem solved after I specify the maloc library path explicitly in my
tcsh environment.
setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib
On 10/08/2015 05:02 PM, Andreas Forster wrote:
Hi Albert,
I apologize that I take your email for a grumpy old
Hi Albert,
I apologize that I take your email for a grumpy old man's rant, but I feel
this mailing list is getting washed out with poorly formulated questions.
What happened to specifying what OS you use, what version of PyMOL, what
version of the apbs plugin. Also, to give answers, it would hel
Hello:
I am trying to calculate the protein surface electstatic properities by
APBS plugin in pymol. But it always failed with messages:
Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?
Does a
Dear PyMOL users,
I'm in trouble in using APBS plugin to display the molecular surface.
The calculations of "set Grid" and "Run APBS" were successfully finished,
but showing the surface by the button of "show" in the Visualization (1) tab
fails with the following message
ObjectMapLoadDXFile: L
Hi Warren,
run pdb2pqr with the "--whitespace" argument to make sure the columns
are separated with whitespace.
If you still want to adjust the coordinates, you can use the
"alter_state" command in PyMOL.
alter_state 1, all, (x,y,z)=(x+100,y+100,z+100)
http://www.pymolwiki.org/index.php/Alter_S
Hi,
I am having trouble running APBS on a structure, and it appears to be
because some of the coordinates are -100 or more negative. This leads to APBS
reading numbers from adjacent columns as concatenated strings because there is
no space between the columns.
This is happenin
z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
int(z*1000)/1000.0)
Cheers,
Warren
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September 21, 2007 7:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Pymol apbs problem
With a certain file 1za1 from pdb when I try to run
With a certain file 1za1 from pdb when I try to run apbs I get the
errors below. Other files are OK. Any suggestions?
error: 1
ValueError Exception in Tk callback
Function: at 0x182892b0> (type: )
Args: ()
Traceback (innermost last):
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymo
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 pro
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
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