[PyMOL] Re: Problems with PyMOL + XIG Summit2.2

[Michael G. <mg...@xi...>]

Warren,

XiG would like to know what is happening with PyMOL and Accelerated-X.
We are not experts with PyMOL so we may need help reproducing the
problem.

WLD>What numeric version of Summit are you using?
WLD>What Summit series do you have (LX, DX, CX, WX, etc.)?
WLD>What operating system, distro, and version are you running?

Most of this information can be generated by running the 'Xsupport'
script and sending the the output.  For instance send the file
'xsupport.txt' that is made by running the command:

  # /usr/X11R6/lib/X11/AcceleratedX/bin/Xsupport > xsupport.txt

This output also contains other information that we might need to
reproduce the problem here.

What GL render mode does PyMOL use while picking objects?

Sincerely,

--
Mike Ginis
mg...@xi...
http://www.xig.com
------------------------------------------------------------------------

On Wed, 21 Jan 2004, Warren L. DeLano wrote:

WLD>PyMOL Users,
WLD>
WLD>It appears that some PyMOL users are having trouble with Xi
WLD>Graphics' Summit line of OpenGL graphics drivers, version 2.2.
WLD>
WLD>Atom picking (which uses glReadPixels with color-encoded pixel
WLD>buffers) fails with these drivers.  It's unclear right now whether
WLD>the problem is due to the XiG OpenGL implementation or with the
WLD>default keyboard modifier event mapping.
WLD>
WLD>If you are both a PyMOL and Summit user (any version), please help by
WLD>responding to me directly with information about:
WLD>
WLD>What numeric version of Summit are you using?
WLD>What Summit series do you have (LX, DX, CX, WX, etc.)?
WLD>What operating system, distro, and version are you running?
WLD>Does atom picking and mouse selection work for you in PyMOL?
WLD>Does PyMOL work fine under XFree86 with the identical hardware setup?
WLD>
WLD>Once we understand the extent of the problem, we'll try to set up our
WLD>own Summit install here and then track down the problem...
WLD>
WLD>Cheers,
WLD>Warren
WLD>
WLD>--
WLD>mailto:wa...@de...
WLD>Warren L. DeLano, Ph.D.
WLD>Principal Scientist
WLD>DeLano Scientific LLC
WLD>Voice (650)-346-1154
WLD>Fax   (650)-593-4020
WLD>
WLD>> -----Original Message-----
WLD>> From: Dr. Daniel James White PhD [mailto:da...@ch...]
WLD>> Sent: Wednesday, January 21, 2004 1:20 AM
WLD>> To: t.g...@ub...; Warren L. DeLano
WLD>> Subject: pymol, with summit2.2 Xserver on linux
WLD>>
WLD>> Hi,
WLD>>
WLD>> I get this problem also.
WLD>> I fear is the the summit Xserver niot handling mouse events properly
WLD>or
WLD>> something.
WLD>> My mouse is a ps2 logitech with a scroll wheel button.
WLD>> I can't do ctrl-click operations.
WLD>>
WLD>> Have you also noticed that your sound does not work with summit, but
WLD>> does with XFree86?
WLD>>
WLD>>   cheers
WLD>>
WLD>> Dan
WLD>>
WLD>>
WLD>> Message: 1
WLD>> From: "Warren L. DeLano" <wa...@de...>
WLD>> To: "'Thierry Granier'" <t.g...@ub...>,
WLD>>     <pym...@li...>
WLD>> Subject: RE: [PyMOL] mouse
WLD>> Date: Fri, 16 Jan 2004 08:12:42 -0800
WLD>>
WLD>> Thierry,
WLD>>
WLD>> This behavior could be the symptom of either malfunctioning OpenGL, o=
r
WLD>a
WLD>> screen with two few colors to support color-encoded picking (which is
WLD>> what PyMOL uses behind the scenes).
WLD>>
WLD>> Please confirm that your display is running in 24 or 32 bit color.  I=
f
WLD>> that is the case and picking still fails, then please try saving a pn=
g
WLD>> file of what you see on the screen ("png filename.png").  If that PNG
WLD>> file exhibits any distortion or artifacts, then that's the cause of
WLD>the
WLD>> problems.  Otherwise, PyMOL may have a bug...
WLD>>
WLD>> Cheers,
WLD>> Warren
WLD>>
WLD>>
WLD>> --
WLD>> mailto:wa...@de...
WLD>> Warren L. DeLano, Ph.D.
WLD>> Principal Scientist
WLD>> DeLano Scientific LLC
WLD>> Voice (650)-346-1154
WLD>> Fax   (650)-593-4020
WLD>>
WLD>> > -----Original Message-----
WLD>> > From: pym...@li... [mailto:pymol-users-
WLD>> > ad...@li...] On Behalf Of Thierry Granier
WLD>> > Sent: Friday, January 16, 2004 12:52 AM
WLD>> > To: pym...@li...
WLD>> > Subject: [PyMOL] mouse
WLD>> >
WLD>> > Good morning,
WLD>> >
WLD>> > I am trying to use pymol on a PC linux RedHat 9.0 using
WLD>> > the software summit 2.2 of Xig, and I run into the following
WLD>> > problem:
WLD>> > after loading a molecule, when I try to click on an atom, for
WLD>> selection,
WLD>> > using
WLD>> > CTRL shif lb or CTRL shift lb, I get the message
WLD>> > "no atom found nearby"
WLD>> >
WLD>> > I have tried all the mouse settings from the gui with no success.
WLD>> >
WLD>> > Any help will be appreciated,
WLD>> > thank you
WLD>> >
WLD>> > Thierry Granier.
WLD>> >
WLD>> >
WLD>> >
WLD>> >
WLD>> > -------------------------------------------------------
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WLD>> > _______________________________________________
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WLD>> > PyM...@li...
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WLD>>
WLD>>
WLD>>
WLD>>
WLD>> Dr. Daniel James White BSc. (Hons.) PhD
WLD>> Cell Biology
WLD>> Department of biological and environmental science
WLD>> PO Box  35
WLD>> University of Jyv=E4skyl=E4
WLD>> Jyv=E4skyl=E4 FIN 40014
WLD>> Finland
WLD>> +358 (0)14 260 4183 (work)
WLD>> +358 (0)414740463 (mob)
WLD>>
WLD>> http://www.chalkie.org.uk
WLD>> da...@ch...
WLD>> wh...@cc...