[PyMOL] pymol and OS X v. 10.3.5 update -- a word of caution

[William Scott]

Hi Folks:

I did the Mac OS X update to v. 10.3.5 yesterday and this changes some
graphics card software. PyMOL now exhibits a really annoying
flickering in rock mode, especially evident when electron density is
being displayed.

I don't know if this is peculiar to my system but if you are
contemplating this update, you might want to think twice. Nothing
positive came of it, but it really messed up this and NFS for me as
well.

HTH someone.

Bill

[Cho, Yoonsang]

Hi Bill,

I also updated to OS X 10.3.5 few days ago. I checked Pymol after read your problem report. I did not
see any flickering during the rock mode. In addition, my NFS is working fine too. Maybe your
problem came from something else.


Regards,

Yoonsang

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I did the Mac OS X update to v. 10.3.5 yesterday and this changes some
graphics card software. PyMOL now exhibits a really annoying
flickering in rock mode, especially evident when electron density is
being displayed.
I don't know if this is peculiar to my system but if you are
contemplating this update, you might want to think twice. Nothing
positive came of it, but it really messed up this and NFS for me as
well.
HTH someone.
Bill

[Warren DeLano]

Following up on Bill's report...

We've updated to version 10.3.5 all the Mac's we have access to and have not
been able to reproduce the reported problem. The configurations tested are:

Mono on an LCD:

MacPYMOL 0.95 on a dual G5 with an ATI Radeon 9600 (RV350)
MacPyMOL 0.95 on a dual G4 with an NVidia GeForce4 Ti 4600
MacPyMOL 0.95 on a G4 laptop with an NVidia GeForce4 MX (440?)

PyMOLX11Hybrid 0.97 on a dual G5 with an ATI Radeon 9600 (RV350)
PyMOLX11Hybrid 0.97 on a dual G4 with an NVidia GeForce4 Ti 4600
PyMOLX11Hybrid 0.97 on a G4 laptop with an NVidia GeForce4 MX (440?) chip

Open-Source PyMOL 0.97 under Fink on a dual G5 with an ATI Radeon 9600
(RV350)

Stereo on a CRT:

MacPyMOL 0.95 on a dual G4 with an NVidia GeForce4 Ti 4600

Yoonsang Cho also reported no problems with the 10.3.5 update, so it appears
that the problem reported is not a blanket systematic problem with the new
MacOS X update, or with any particular brand of video card. Nevertheless,
since Bill is apparently experiencing a real problem, caution may still be
warranted until the situation becomes more clear.

Cheers,
Warren

--
mailto:***@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax [phone]

-----Original Message-----
Behalf Of William Scott
Sent: Tuesday, August 10, 2004 2:58 PM
Cc: CCP4 bulletin board
Subject: [ccp4bb]: pymol and OS X v. 10.3.5 update -- a word
of caution
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I did the Mac OS X update to v. 10.3.5 yesterday and this
changes some graphics card software. PyMOL now exhibits a
really annoying flickering in rock mode, especially evident
when electron density is being displayed.
I don't know if this is peculiar to my system but if you are
contemplating this update, you might want to think twice.
Nothing positive came of it, but it really messed up this and
NFS for me as well.
HTH someone.
Bill

[William Scott]

What Mac generation are you using, and what video card specifically?

GeForce4 Ti 4600


Machine Model: Power Mac G4
CPU Type: PowerPC G4 (3.2)
Number Of CPUs: 2
CPU Speed: 1.25 GHz
L2 Cache (per CPU): 256 KB
L3 Cache (per CPU): 2 MB
Memory: 2 GB
Bus Speed: 167 MHz
Boot ROM Version: 4.4.7f1

Following up on Bill's report...
MacPyMOL 0.95 on a dual G4 with an NVidia GeForce4 Ti 4600

... which I think is the same thing. So I will investigate further.
Sorry for any trouble this has caused.

[Luca Jovine]

Hi Bill,

You might try to see whether you can fix the problem by re-installing
the 10.3.5 update, not through Apple's Software Update (which you most
likely won't be able to do anyway, if this is how you installed it the
first time), but by downloading the full 10.3.5 combined updater (88
MB) from here:

http://www.apple.com/downloads/macosx/apple/
macosxcombinedupdate_10_3_5_.html

and manually launching the updater. Surprisingly enough, in this way
you can re-install 10.3.5 on top of itself. This is because, as
explained here:

http://www.macfixit.com/article.php?story=20040811021537993

there seem to be 3 (3!) different version of the 10.3.5 updater,
weighting 23, 43 and 88 MB respectively (the 23MB is the one that gets
installed by Software Update if you previously had 10.3.4)... and
certain third-party (as well as users like you and I, who just can't
help tinkering with the system ;-) ) may require the installation of
the bigger version for things to go smoothly.

I had a couple of different issues after updating to 10.3.5 via
Software Update, one of which was that the screen occasionally filled
with colored rectangles for a second or so, upon waking from sleep. The
other was a problem with mail. Both were solved upon manually
re-installing 10.3.5 using the 88 MB updater.

Just a suggestion...

Ciao Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Brookdale Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620 FAX: +1.360.926-1823
E-Mail: ***@mac.com - ***@mssm.edu
W3: http://www.mssm.edu/students/jovinl02
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