Re: [PyMOL] APBS problem

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

[PyMOL] APBS problem

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

Re: [PyMOL] APBS problem

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

[PyMOL] APBS problem on showing the molecular surface

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:

Re: [PyMOL] APBS problem

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)

[PyMOL] APBS problem

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

[PyMOL] Pymol apbs problem

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: function lambda at 0x182892b0 (type: type 'function') Args: () Traceback (innermost last): File

Re: [PyMOL] Pymol apbs problem

_ 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

Re: [PyMOL] Pymol apbs problem

, Warren _ 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

[PyMOL] apbs problem

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

Re: [PyMOL] apbs problem

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