Re: [PyMOL] wierd bug in Ubuntu 12.10

2012-12-16 Thread lloyd riggs 

Dear All,

I have a wierd bug with pymol after a recent update to Ubuntu 12.10.  If I use 
any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then 
does some sort of switch if it is open at the same time for selections.  It 
changes from residue, to atom, to whole molecule in the selection, depending on 
how much or how many times you go and type something in gedit.  It then does 
not allow you to rotate the molecule, or change the menu selections anymore.  I 
then have to re-start the computer, or re-install pymol to re-set the normal 
operations.  This is extremely problematic, as pymol is a good program to 
quickly look at specific residues, etc...when doing massive text based 
tabulations of specific residues, and a necessary orientation and check 
visually is needed on the side to keep track of things.  Needless to say the 
uses for anything else, such as making images, etc..

Has anyone experienced this, or more importantly, does anyone have a patch or 
bug fix.

Sincerely,

Stephan Watkins

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Re: [PyMOL] Rendering memory errors

2012-12-08 Thread lloyd riggs 

Dear All,

I put off upgrading to Ubuntu 12.04 as this happens every time I upgrade with 
half my things (software).  In any case...

I am no longer able to use the rendering plugin , which is a vlauble asset as I 
am at this moment in the midst of making some publication quality figures.

Additional, the standard ray trace option will only work if I use a white 
background, and zoom out further than would make a good image, ie a 300 amino 
protein about 1 inch square on an 8x8 inch window (visual field).

I tried standard things, such as updating pymol, manually installing pymol 1.5 
, etc...and the same bug prevades.

As it is both the rendering types, I assume it is some change to memory 
utilized by the shaders, as it crashes everytime.  I have a similar problem now 
with gimp as well, however the memory cap is easy to see and maxes out around 
3-4 G before crashing, however there is a 16 G memory, along with 4G on the GPU 
so I do not know where the errors come from.  I do not get the errors on VMD, 
however prefer Pymol for the ease of use and also the images are nice.

Any suggestions on how to fix this would be appriciated.  I also posted a bug 
on ubuntu, but the responses of such are limited, ie a general posting on bugs 
rather than maillists...

Sincerely,

Stephan Lloyd Watkins

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