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#112 png command does nothing

v1.4.1
closed
5
2012-03-05
2011-11-29
freeseek
No

I am trying to export a png image of what I see within PyMOL but nothing happens. I try the command
png /tmp/ex.png
but no /tmp/ex.png file is created. I am using Ubuntu 11.10 on a 64 bits machine and PyMOL 1.4.1.

Discussion

  • Jason Vertrees

    Jason Vertrees - 2011-11-30
    • assigned_to: nobody --> inchoate
     
  • Jason Vertrees

    Jason Vertrees - 2011-11-30

    Thanks for the bug report. Does PyMOL emit any error message like: ScenePNG-Error: error writing "/tmp/foo/bar.png"! Please check directory...

    What happens if you try:

    png /tmp/ex.png, ray=1

    There used to be a bug in PyMOL where when the image wasn't ray traced the buffer wasn't copied properly.

     
  • freeseek

    freeseek - 2011-11-30

    Nothing happens even with
    png /tmp/ex.png, ray=1
    The annoying thing is that no file is created and no error is thrown whatsoever.
    Just really nothing at all happens.

     
  • Jason Vertrees

    Jason Vertrees - 2011-11-30

    How did you install v1.4.1?

    This is hard to debug without access to the machine or any error messages. I've personally tested v1.4.1 on Ubuntu 11.04 and 11.10 and it worked fine. I'll keep looking into it.

    Anything else about the machine, setup, install I should know?

     
  • freeseek

    freeseek - 2011-11-30

    Not sure how to help here. I am using the pymol included with Ubuntu (that is, I installed with "apt-get install pymol"). I will try my machine at home later which is also using Ubuntu 11.10.

    I also tried to install the svn branch with
    svn co https://pymol.svn.sourceforge.net/svnroot/pymol pymol
    Changed the layer3/Executive.c occurrence of ce_types.h to ../modules/cealign/src/ce_types.h
    and then run
    ./configure
    make install
    ./pymol
    But I got the error
    Traceback (most recent call last):
    File "/tmp/pymol/trunk/pymol/modules/launch_pymol.py", line 32, in <module>
    import pymol
    File "/tmp/pymol/trunk/pymol/modules/pymol/__init__.py", line 472, in <module>
    import _cmd
    ImportError: /pymol/trunk/pymol/modules/pymol/_cmd.so: undefined symbol: ObjectVolumeSetRamp

     
  • Jason Vertrees

    Jason Vertrees - 2011-11-30

    It's best to build as follows:

    svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
    cd pymol
    sudo python setup.py install
    sudo python setup2.py install

    then follow the directions printed on the screen. PyMOL doesn't make well from ./configure && make && make install.

     
  • Jason Vertrees

    Jason Vertrees - 2011-12-06

    Freeseek, please pull the latest PyMOL code and try again.

     
  • Jason Vertrees

    Jason Vertrees - 2011-12-06

    Freeseek, actually, please try:

    png fileName.png, prior=1

    Thanks.

     
  • Jason Vertrees

    Jason Vertrees - 2012-03-05
    • status: open --> closed
     

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