[PyMOL] pymol beta31 segfault with nvidia

[Dmitriy]

Hello

I've tried latest 0.99beta31 from cvs. It does segmentation fault on my linux 
Mandriva 2006 with nvidia 81.74 drivers.

 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: GeForce3/AGP/SSE/3DNOW!
  GL_VERSION: 1.5.5 NVIDIA 81.74
zsh: segmentation fault 

version 0.99beta29 works fine with the same driver.
tried on Fedora Core 4 with Mesa 6.2.1, beta31 works fine.

so it seems to be a problem with nvidia driver. not sure about 7676.

  Thanks
 Dmitriy

[PyMOL] cvs version of pymol does not run

[Dmitriy]

Hello

I've downloaded a new version from cvs. It compiles, but do not run.

$ python /home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/__init__.py
Traceback (most recent call last):
  File "/home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/__init__.py", 
line 341, in ?
import _cmd
ImportError: /home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/_cmd.so: 
undefined symbol: TypeInit

What is this "TypeInit" ?
beta29 compiles and runs on Mandriva 2006 and Fedora Core 4.
Latest from cvs do not.

Does anyone have the same problem?
Thanks
   Dmitriy

[PyMOL] .xyz file loading problem from chempy module

[Dmitriy]

Hello everyone

It seems to be a problem with loading an .xyz file as a chempy model.
For example doing

from chempy import io
m = io.xyz.fromFile("some.xyz")

gives:

chempy: reading "some.xyz".
Traceback (most recent call last):
  File "", line 1, in ?
  File "/home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py", 
line 185, in fromFile
TypeError: fromList() takes exactly 1 argument (2 given)

If I've got the right idea whats going on, there should be  
fromList(self,list)  function in xyz.py which will hide the Storage one.
Like it's done in pdb.py (it works fine for io.pdb.fromFile)

I'm trying to establish a communication between my program and pymol in a 
simple .xyz format. Sending a list of strings, creating a chempy model and 
loading it into pymol will work. If there is some workaround or a fix for 
problem mention above.

Warren, Is it possible to implement a way of passing .xyz file as a string, 
not as a list of strings or a file? I've seen molstr, pdbstr etc. but not 
xyzstr. 
And a short description how to load pdbstr for example it in this way will be 
great.

Thanks
  Dmitriy

[PyMOL] cmd.quit() kills pymol together with the external python launcher

[Dmitriy]

Hello

I have a question about cmd.quit() behavior.
here goes simplest example:
-
import __main__
__main__.pymol_argv = [ 'pymol', '-qx' ]

import pymol
pymol.finish_launching()

from pymol import cmd

raw_input("type something")
cmd.quit()
print "finfished"

cmd.quit() kills the whole program, not just PyMol's window.
i.e. "finished" is never printed.
Is it possible somehow to close only PyMol without interrupting the program?
 
What I want to be able to do in general is to launch PyMol from my program, 
plot some data then close PyMol. Then launch PyMol again if I need to plot 
some things again, plot, close, and so on.  All these things related to PyMol 
are separated in a class. Calling cmd.quit() simply ruins the whole program.

Pymol ver. 20beta I think (latest from CVS)

Help is really appreciated
Thanks
Dmitriy

[PyMOL] launching PyMol from a python function

[Dmitriy Igor Bryndin]

I'm trying to start PyMol from another python program.
After the 0_99beta17 it is possible to start it from the __main__ part of a 
code. But when I start PyMol from a function 'pymol.finish_launching()' goes 
in an endless loop. 


Here goes an example:
---
def funct():
  import __main__
  __main__.pymol_argv = [ 'pymol', '-qx' ]
  import pymol
  pymol.finish_launching()
  print "finished" 


if __name__ == '__main__':
  funct()
---
In this case PyMol window starts, but program never reaches 'print 
"finished"'. 


The same time
---
if __name__ == '__main__':
  import __main__
  __main__.pymol_argv = [ 'pymol', '-qx' ]
  import pymol
  pymol.finish_launching()
  print "finished"
---
works fineand prints "finshed" 


after getting into PyMol's finish_launching()  (inside __init__.py)
while not hasattr(__main__,'pymol'):
  e.wait(0.01)
Goes in an endless loop.
I've tried   print dir(__main__)   just before this loop. When PyMol is 
launched not from a function, __main__ indeed have attributes '__main__' and 
'pymol'.  Launched from a function, there are no '__main__' or 'pymol', but 
'funct'. 

I'll really appreciate any help or hints how make it possible to launch 
PyMol from a function or from a method of some class. 


 Dmitriy

[PyMOL] PyMol segmentation fault while starting from external python program

[Dmitriy Igor Bryndin]

Launching PyMol form external python script will produce segmaentation 
fault.

For example starting "launch.py" from "/pymol/examples/launching"
--
$ python launch.py
zsh: segmentation fault  python launch.py
--
Crashes without even showing PyMol windows. 


Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The same story.
Different pythons and compiling different versions of PyMol does not change 
anything. 


It will launch PyMol windows if there is only
  import pymol
line. 


Adding
  pymol.finish_launching()
or
  from pymol import cmd
  cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
will produce segmentation fault. With no windows shown. 

The same time if I'll try to debug step by step, let's say, "launch_demo.py" 
(from "/pymol/examples/launching")

---
pymol.finish_launching()
from pymol import cmd
cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
cmd.show("sticks")
---
using IDLE. Everything will work. It starts windows, loads a file, changes 
to sticks...
Running it "python launch_demo.py" will wait for a second and return 
segmentation fault. 

If someone knows what's going on, please help me. 


Thanks
  Dmitriy Bryndin 

[PyMOL] PyMol does not compile with python 2.4.1

[Dmitriy Igor Bryndin]

I've tried to compile PyMol 0.99beta15 (one from CVS)
using:
python setup.py install 

it fails while comiling layer0/Crystal.c 


the problem in gcc  "-Wp,-D_FORTIFY_SOURCE=2" parameter, which fails
compilation of PRINTF macro inside of Crystal.c 

If I compile Crystal.c without this parameter everything is fine. 


The python is 2.4.1 which comes with Fedora Core 4.
gcc version 4.0.1 20050727 (Red Hat 4.0.1-5) 


I can't find a nice way of getting rid of this "-Wp,-D_FORTIFY_SOURCE=2"
parameter without getting inside python and killing it manually.
If someone knows the way, it will be helpful.
But the main question is WHY it does not compile. Is it somthing wrong
with PyMol code?
As much as I know, this parameter do additional code checks for things like
buffer owerflow. Which itent to be useful. 


Thanks
  Dmitriy Bryndin 



it fails with this error:
--
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE 
-D_PYMOL_INLINE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 
-Ilayer4 -Ilayer5 -I/usr/include/python2.4 -c layer0/Crystal.c -o 
build/temp.linux-i686-2.4/layer0/Crystal.o -ffast-math -funroll-loops -O3

In file included from /usr/include/python2.4/Python.h:8,
   from layer0/os_python.h:26,
   from layer1/Setting.h:19,
   from layer1/CGO.h:21,
   from layer0/Crystal.c:21:
/usr/include/python2.4/pyconfig.h:835:1: warning: "_POSIX_C_SOURCE" 
redefined

In file included from /usr/include/stdio.h:28,
   from layer0/os_std.h:23,
   from layer0/Crystal.c:18:
/usr/include/features.h:150:1: warning: this is the location of the previous 
definition
layer0/Crystal.c:314:1: error: unterminated argument list invoking macro 
"sprintf"

layer0/Crystal.c: In function ‘CrystalDump’:
layer0/Crystal.c:201: error: syntax error at end of input
error: command 'gcc' failed with exit status 1
--