[PyMOL] Re:2 questions about Summit drivers w/ Radeon8500 card for stereo...

2003-06-04 Thread Dr. Daniel James White PhD
Hi, Sounds line you didn't have a correct installation of the Xig summit2.2??? I thought the installation was supposed to move all the old mesa/GL stugff to a back up and replace them with the acellerated xig ones? Have you contacted the guys at Xig? If you have paid the 99 dollars or

Re: [PyMOL] Nuvision stereo glasses?

2003-07-18 Thread Dr. Daniel James White PhD
Hi David, ATI radeon 8500 works with the xig.com Summit Xserver, with stereographics stereo enabler cable (takes sync from the monitor cable) and infra red emitter box E2 with stereographics infra red shutter glasses. i don't know if this emitter and enabler cable work with nuvision glasses?

[PyMOL] pymol crash on linux opening a .pse saved session file

2003-08-06 Thread Dr. Daniel James White PhD
Hi Warren and all, My student is experiencing a crash every time she attempts to open a .pse saved session file. The file is of a large trimeric molecule in a cartoon and space fill representation with different coloured domains Hardware: PC, Athalon, 1gb ram, ATI radeon 8500 video card, 2

[PyMOL] Re: ATI radeon 8500 and Linux quad buffered stereo

2003-09-02 Thread Dr. Daniel James White PhD
is a digital video output and I need to shop for the stereo enabler cable... ulrich Re: [PyMOL] Nuvision stereo glasses? * From: Dr. Daniel James White PhD d...@removethischalkie.org.uk * Date: Fri, 18 Jul 2003 11:59:17 +0300 * In-reply-to: e19dlwr-0005zt...@sc8-sf-list2

[PyMOL] energy minimisation in python

2003-09-10 Thread Dr. Daniel James White PhD
Warren , Are you aware of the python MMTK molecular dynamics package? AMBER force field and energy minimisation are there! Could this be easily interfaced with pymol? http://starship.python.net/crew/hinsen/MMTK/ I had a play with it but I don't really know what I am doing and need to

[PyMOL] Re: Need advice on graphic card

2003-11-12 Thread Dr. Daniel James White PhD
Hi, I have 2 monitors running out of an ATI Radeon 8500 on redhat 8.0 using the summit accelerated Xserver from Xig.com for hardware stereo on one of the monitors. I use the dual view function, so 1 big desktop (1 screen on 2 monitors) Very hardware accelerated! cheers Dan On 12 Nov

[PyMOL] rebuilding icosohedral virus structure - symexp?

2004-04-02 Thread Dr. Daniel James White PhD
Hi, I have a virus envelope protein structure pdb entry, and I want to rebuild the whole virus protein shell using the symmetry transformations given in the 180 (60 trimers) REMARK 350 BIOMT1 1 1.0 0.0 0.0 REMARK 350 BIOMT2 1 0.0 1.0 0.0 REMARK 350 BIOMT3 1

Re: [PyMOL] save icosohedral virus structure with all subunits present?

2004-04-02 Thread Dr. Daniel James White PhD
. ~Todd Geders On Fri, 2004-04-02 at 07:14, Dr. Daniel James White PhD wrote: Hi, I have a virus envelope protein structure pdb entry, and I want to rebuild the whole virus protein shell using the symmetry transformations given in the 180 (60 trimers) REMARK 350 BIOMT1 1 1.0 0.0 0.0

[PyMOL] Re: split_states

2004-04-06 Thread Dr. Daniel James White PhD
Warren, Exactly what I needed! cheers Dan On 5 Apr 2004, at 23:08, pymol-users-requ...@lists.sourceforge.net wrote: Message: 10 From: Warren DeLano war...@delanoscientific.com To: 'Todd Geders' ged...@purdue.edu, 'Ann Mullin' amul...@tulane.edu Cc:

[PyMOL] save all not working for multiple objects from split_states?

2004-04-06 Thread Dr. Daniel James White PhD
Hi all, I opened a biological unit pdb file of a viral capsid protein containing the 60 states or models making up the whole viral capsid structure. I did split_states to get all 60 molecules as individual objects sweet! then I deleted the ones I didnt want, leaving 15 molecules around one

[PyMOL] Re: give unique chain identifiers

2004-04-14 Thread Dr. Daniel James White PhD
segi 0001 http://delsci.com/img/1c8e-subunit.jpg Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Daniel James White PhD Sent: Tuesday, April 06, 2004 6:22 AM To: pymol-users

[PyMOL] enable direct rendering DRI on fedora core 2

2004-06-11 Thread Dr. Daniel James White PhD
Hi everyone! how can I enable direct rendering DRI on fedora core 2? I have an ATI radeon 8500 LE, Should I use the redeon driver, or the r200 driver? I edited my xorg.conf file is as below, but VMD and pymol tells me I am still using indirect mesa rendering, and it is SLOW. the ATI

[PyMOL] ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520???

2004-08-25 Thread Dr. Daniel James White PhD
Hi has anyone had any luck getting quad buffered stereo with the new ATI linux drivers, fglrx 3.11 I wondered if any one has a working XFree86 config file? my setup is ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel (fedora core 2), trying to get quad buffered stereo on

[PyMOL] sony (sgi) monitorGDM-20D11 flashing LEDs, no picture

2004-09-02 Thread Dr. Daniel James White PhD
Hi there, Just on the off chance that someone might know... We have a sgi indigo2 that is working, but the monitor seems to have a problem its a sony (sgi) GDM-20D11 There is no picture when it is turned on, and the green and amber LEDs next to each other on the bottom right of the

[PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

2004-09-16 Thread Dr. Daniel James White PhD
Hi Warren and all, I'm trying building pymol on sgi irix 6.2 gcc 2.95.2 (I got root access to that old sgi indigo2 extreme irix 6.2, and got a 13W3 to VGA cable to connect it to my sony g520 monitor, and it works great.) I installed gcc2.95.2, and am building the external dependencies for

Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2

2004-09-17 Thread Dr. Daniel James White PhD
...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Daniel James White PhD Sent: Thursday, September 16, 2004 10:41 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2 Hi Warren and all, I'm trying building

Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2, external sources python build fails

2004-09-17 Thread Dr. Daniel James White PhD
Hi all, building pymol external sources on irix6.2 with gcc 2.95 tcl and tk and zlib build ok!!! but python fails at the first hurdle with: creating Makefile cd /usr/people/dwhite/freestuff/pymolstuff/ext-0_95/src/Python-2.3.3; make cc -n32 -c -OPT:Olimit=0 -DNDEBUG -O -I.

[PyMOL] Re: hardware stereo in IRIX

2005-04-23 Thread Dr. Daniel James White PhD
Hi Nicolas, I have the same SGI computer, Indigo 2 Impact 1 running IRIX 6.5.22m (BTW upgrade to this release is free from supportfolio at SGI, might have to install patch 5086 first) I have stereo graphics emitter and glasses, and stereo works fine, i just double click a link on my