[PyMOL] cannot run Pymol as standard user

[Yanni]

Hello everyone

I'm new to Pymol and I'm having problems running it as a standard user.

I have a mac mini and I installed Pymol using homeBrew, the free package 
manager for OSX. The installation
was done while logged in as administrator and it works fine but when I 
login as a standard user and type "pymol" on the command-line, I get the 
following error:


Traceback (most recent call last):
   File 
"/usr/local/Cellar/pymol/1.7.6.0_1/libexec/lib/python2.7/site-packages/pymol/__init__.py",
 
line 71, in 
 import pymol
   File 
"/usr/local/Cellar/pymol/1.7.6.0_1/libexec/lib/python2.7/site-packages/pymol/__init__.py",
 
line 521, in 
 import pymol._cmd
ImportError: 
dlopen(/usr/local/Cellar/pymol/1.7.6.0_1/libexec/lib/python2.7/site-packages/pymol/_cmd.so,
 
2): Library not loaded: /opt/X11/lib/libpng15.15.dylib
   Referenced from: 
/usr/local/Cellar/pymol/1.7.6.0_1/libexec/lib/python2.7/site-packages/pymol/_cmd.so
   Reason: Incompatible library version: _cmd.so requires version 39.0.0 
or later, but libpng15.15.dylib provides version 34.0.0


If anyone can help me please let me know what I have to do.

Many thanks



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Re: [PyMOL] weird behavior with renitialize

[Thomas Holder]

Hi Blaine,

I confirm, this is a regression bug in PyMOL 1.6.

This will only happen when using PyMOL commands, not when doing the same thing 
with a Python script. Here is an equivalent replacement for your alias:

python
from pymol import cmd, preset
@cmd.extend
def q1():
cmd.reinitialize()
cmd.fetch('3v6d', 'HIVrt', type='pdb')
preset.ball_and_stick("c. P and i. 822")
cmd.zoom('c. P and i. 822')
cmd.rock() 
python end

Cheers,
  Thomas

On 11 Feb 2016, at 09:55, Mooers, Blaine H.M. (HSC)  
wrote:

> Dear PyMOLers,
> 
> I am using incentive version 1.8.0.5.  I made the following python script 
> with an alias
> 
> from pymol import *
> cmd.alias('q1', 'delete all;fetch 3v6d, HIVrt, type=pdb, 
> async=0;preset.ball_and_stick("c. P and i. 822");zoom c. P and i. 822;rock') 
> 
> Repeated entry of the alias name changes the color scheme of the atoms and 
> toggles on and off the rocking motion.
> Apparently, the settings are not reset with "delete all".
> 
> If I replace "delete all" with "remove all" or 'reinitialize", the command 
> history windows shows thepdb file haveing been fetched but no molecular 
> object show ups in the internal gui. In version 1.55, reinitialize works as 
> expected. 
> 
> It seems that the reinitialize needs a "pause until completed signal" like 
> "async=0 " in fetch or theunix "&&".  
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Assistant Professor
> Director of the Laboratory of Biomolecular Structure and Function
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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