[PyMOL] Re:2 questions about Summit drivers w/ Radeon8500 card for stereo...
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 whatever it costs, then their support is usually prompt and effective! Lack of DRI means your graphics hardware is not being used at full speed! On my RH8.0 box, the radeon 8500 64MB with Xig summit 2.2 is working really well for quad buffered stereo. Haven't are upgrade to RH9 yet. I keep hearing about problems! cheers Dan On Wednesday, June 4, 2003, at 01:03 AM, pymol-users-requ...@lists.sourceforge.net wrote: Message: 10 Date: Mon, 02 Jun 2003 14:31:08 -0700 From: Cameron Mura cm...@ucsd.edu Reply-To: cm...@ucsd.edu Organization: UCSD To: pymol-users@lists.sourceforge.net, o-i...@origo.imsb.au.dk CC: Cameron Mura cm...@mccammon.ucsd.edu Subject: [PyMOL] 2 questions about Summit drivers w/ Radeon8500 card for stereo... Dear PyMOL and O list members, I just got stereo working on my machine (PC, Red Hat 9, Radeon8500 (64MB) video card) after installing Xi Graphic's Summit v2.2 DX-Platinum drivers to enable quad-buffered software stereo, but I noticed that 3D stereo rendering in 'PyMOL' and 'O' seems a lot slower than it used to be (same hardware, but w/ Mandrake and v2.1 Summit drivers). So, I have 2 questions (that may or may not be related to the sluggishness): (1) After installing xvsc and summit drivers, is any further configuration required to insure proper usage of the Accelerated-X openGL libraries, include files, etc.? I ask this because I noticed that GL-based programs such as PyMOL are NOT using the Accelerated-X library libXda.so.1... For example, if I type ldd /usr/X11R6/bin/xglinfo I get the following: [r...@cm1 etc]# ldd /usr/X11R6/bin/xglinfo libGLU.so.1 = /usr/lib/libGLU.so.1 (0x4002d000) libGL.so.1 = /usr/X11R6/lib/sav-GL/libGL.so.1 (0x400b2000) libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x40125000) libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x40134000) libm.so.6 = /lib/tls/libm.so.6 (0x40213000) libc.so.6 = /lib/tls/libc.so.6 (0x4200) libpthread.so.0 = /lib/tls/libpthread.so.0 (0x40235000) libdl.so.2 = /lib/libdl.so.2 (0x40243000) /lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x4000) I guess I could remove the paths to the old mesa GL libraries and include files (/usr/include/GL/sav-GLinc/ and /usr/X11R6/lib/sav-GL/) from /etc/ld.so.conf, but then other GL-based applications don't seem to work?? So, is there anything special i need to do in order to make the libXda.so.1 module used instead of the standard Mesa openGL ones??? (2) Upon start-up, GL-based applications give the following line: Xlib: extension XFree86-DRI missing on display :0.0. I'm wondering what this problem means (if anything), and how it may be corrected?? Thanks for any advice! Cameron Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] Nuvision stereo glasses?
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? (this commercial X server seems to break my sound though.confirmed to me by xig as a bug) cheers Dan On Friday, July 18, 2003, at 06:28 AM, pymol-users-requ...@lists.sourceforge.net wrote: --__--__-- Message: 4 Date: Thu, 17 Jul 2003 17:51:27 -0400 From: David A. Horita dhor...@wfubmc.edu To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Nuvision stereo glasses? This is a multi-part message in MIME format. --_=_NextPart_001_01C34CAD.92AD614C Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or = QuadroFX 500 cards under linux? Or any other non-nVidia card which = supports quad-buffered stereo but doesn't have a mini-din connector = on-board (i.e., not the 256 Mb FireGL X1). It would be nice to avoid = the problems with the nVidia stereo drivers, but I'd rather not buy the = FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and hard to = find). The Nuvision guys told me that their VGA passthrough (the -100 = model, not the -NSR model), picks up the stereo sync from nVidia cards = coming through the 15-pin VGA connector. Is this signal present on ATI = cards (or even on dual-DVI-I output cards)? =20 Thanks, Dave Horita =20 -=20 David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016=20 Tel: 336 713-4194 Fax: 336 716-7671=20 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/ =20 Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] pymol crash on linux opening a .pse saved session file
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 monitors dual head. OS: Redhat 8.0, Xig.com Summit 2.2 X-server for hardware stereo. software: pymol-0.90-1.rh8.0.py22 RPM installation On loading the .pse file the computer thinks for a bit, and it looks like when it attempts to display the molecule the viewing window resizes to that which was saved, then the screen goes weird on the monitor the viewing window is on, the mouse pointer vanished and the keyboard is non responsive, forcing us to press the reset button to reboot. Looks like a big Xserver crash. Any ideas? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] Re: ATI radeon 8500 and Linux quad buffered stereo
Hi, Indeed you should just need the enabler cable from stereographics. This is compatible with emitter box E-2, and not other emitters I think? with the hardware browser in gnome menu - system tools my card is listed as Radeon R200 QL (Radeon 8500 LE) and in the Xig.com Xserver Xsetup program as ATI RADEON 8500, 64MB The enabler cable fits into the normal (not digital / flat panel...?) monitor socket in the back of the card inbetween the monitor cable and the card. Also the emitter box is powered from the keyboard port.weird, but seems to work. The enabler cable acts as kind of a splitter for the keyboard port, so you can plug in the keyboard and the emitter box. I have a second CRT monitor running out of the digital/flat panel port of the card, using the converter that came with the card. In Xsetup I have enabled dual view in horizontal mode... and it works. I think the stereo display is a little slower of course since the card is doing more work, but I can have a 3D window covering all my big monitor, and control windows on the other smaller monitor, making up I large rectangular screen. both monitors are running at 1280x1024. millions of colours. good luck! Dan On Monday, September 1, 2003, at 09:41 PM, Ulrich Englich wrote: Dear Daniel: Googlegoogle... Now I found this at the PyMol discussion group... I guess that answers pretty much my quetions. I presume we are talking about the exact same graphics card? The connector to the left 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.sourceforge.net * List-archive: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users * List-id: PyMOL Users Group pymol-users.lists.sourceforge.net * List-post: mailto:pymol-users@lists.sourceforge.net 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? (this commercial X server seems to break my sound though.confirmed to me by xig as a bug) cheers Dan -- -- \|/ (o o) --oOO--(_)--OOo- www.macchess.cornell.edu Dr. Ulrich Englich Tel: 607-255 9386 209 Biotechnology Building Fax: 607-255 6249 Ithaca, New York 14853E-mail: u...@cornell.edu *** This message was written entirely with recycled electrons *** Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] energy minimisation in python
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 learn Dan On Tuesday, September 9, 2003, at 09:08 PM, pymol-users-requ...@lists.sourceforge.net wrote: We'd all like to see a real forcefield in PyMOL, but no one has written the code yet. Cheers, Warren Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] rebuilding icosohedral virus structure - symexp?
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 0.0 0.0 1.0 REMARK 350 BIOMT1 2 0.80900 0.30900 0.5 REMARK 350 BIOMT2 2 etc... REMARK 350 BIOMT3 2 etc... etc.. lines of the pdb file. These lines give the transformations to give the complete protein spherical capsid structure. can I use pymol symexp command to do this? I tried loading the file then doing symexp sym=1ch8h,(1ch8h),20 but nothing seemed to happen? I'm doing it wrong i'm sure. I did manage to do this in SwissPDBViewer, but I cant save the complete capsid structure as a file that Bodil reads properly. Pymol of course reads the file ok... So suppose it is a bodil problem... anyway, can i use symexp to do this automatically. you have to do it by hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i did it on a mac) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] save icosohedral virus structure with all subunits present?
Ok, biological unit, thats great! but now, how do I save this virus capsid as a a pdb or mol file where each of the many subunits have a different chain identifier. When I save the virus caspid structure with all subunits visible, the pdb file still only has on subunit in it, not all of them... I want to open it in Bodil (or Pymol or whatever) and only view the chains I want to see. I just want to see the subunits around one of the 5 fold symmetry axes, ie with the 5 fold axis in the middle surrounded by the 5 trimers/triangles that surround the 5 fold axis. cheers Dan On 2 Apr 2004, at 17:57, Todd Geders wrote: I've found the easiest way to do this under PyMOL is to download the Biological Unit version of the PDB file. They've already regenerated the virus particle for you. It will only show one of the particles at a time unless you check Movie-Show All States. ~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 REMARK 350 BIOMT2 1 0.0 1.0 0.0 REMARK 350 BIOMT3 1 0.0 0.0 1.0 REMARK 350 BIOMT1 2 0.80900 0.30900 0.5 REMARK 350 BIOMT2 2 etc... REMARK 350 BIOMT3 2 etc... etc.. lines of the pdb file. These lines give the transformations to give the complete protein spherical capsid structure. can I use pymol symexp command to do this? I tried loading the file then doing symexp sym=1ch8h,(1ch8h),20 but nothing seemed to happen? I'm doing it wrong i'm sure. I did manage to do this in SwissPDBViewer, but I cant save the complete capsid structure as a file that Bodil reads properly. Pymol of course reads the file ok... So suppose it is a bodil problem... anyway, can i use symexp to do this automatically. you have to do it by hand 1 by 1 in SwissPDBviewer (and the linux version is a bit funny...i did it on a mac) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id70alloc_id638opÌk ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] Re: split_states
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-users@lists.sourceforge.net Subject: RE: [PyMOL] biological unit question Date: Mon, 5 Apr 2004 13:07:13 -0700 Todd, Try MacPyMOL for the full PYMOL effect. http://delsci.com/macpymol There is also a new command in the 0.95 series: split_states object-name which will spread a PDB biological unit (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with all_states = 1. load 1c8e.pdb1, 1c8e split_states 1c8e delete 1c8e zoom spectrum b hide lines set cartoon_sampling,3 show cartoon bg_color grey70 set hash_max, 150 ray ... orient zoom complete=1 ray image screen-shot at: http://delsci.com/img/1c8e.jpg http://delsci.com/img/1c8e-screen.jpg Note that looking at large systems such as this (255300 atoms) may take some extra RAM -- 1.5 GB is recommended for this task, and it still takes a dual 2 Ghz G5 85 seconds to render... Cheers, Warren Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] save all not working for multiple objects from split_states?
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 of the 5 fold symmetry axes. now I want to save these molecules to a pdb file. so I did save 5fold.pdb, all this gave no errors, but the pdb file written only contains END what am I doing wrong? I expect it is my simple mistake? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] Re: give unique chain identifiers
Hi Warren, OK, that works just as you say it does. however, what I really need is each chain to have a unique chain identifier in the pdb file written out. I see there might be a problem here as there are 60 molecules, and only 24 letters in the alphabet I actually only want to have 15 of them in my model, so we could get round it that way, by deleting the ones I dont want but then how to give them unique pdb chain identifiers? I want to load the 15 molecule model in Bodil to do my actual modelling. cheers Dan On 6 Apr 2004, at 21:36, Warren DeLano wrote: Dan, That's the not expected result, but indeed you have a problem -- each of those subunits will have identical atoms. To resolve this, assign a unique segment identifier to each subunit: load 1c8e.pdb1, 1c8e split_states 1c8e delete 1c8e alter all, segi = model[-4:] rewind save test.pdb, all dele all load test.pdb The reason why you were getting a PDB file with just END is that you didn't return the viewer ro frame/state 1 after moving all of the data to state 1. After the above, you'll now be able to address each subunit indepently as: hide show ribbon color red, segi 0001 zoom 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@lists.sourceforge.net Subject: [PyMOL] save all not working for multiple objects from split_states? 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 of the 5 fold symmetry axes. now I want to save these molecules to a pdb file. so I did save 5fold.pdb, all this gave no errors, but the pdb file written only contains END what am I doing wrong? I expect it is my simple mistake? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id70alloc_id638op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] enable direct rendering DRI on fedora core 2
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 closed source driver doesn't work on the fedora 2.6 kernel so I cant use that. cheers Dan # XFree86 4 configuration created by pyxf86config Section ServerLayout Identifier Default Layout Screen 0 Screen0 0 0 InputDeviceMouse0 CorePointer InputDeviceKeyboard0 CoreKeyboard EndSection Section Files # RgbPath is the location of the RGB database. Note, this is the name of the # file minus the extension (like .txt or .db). There is normally # no need to change the default. # Multiple FontPath entries are allowed (they are concatenated together) # By default, Red Hat 6.0 and later now use a font server independent of # the X server to render fonts. RgbPath /usr/X11R6/lib/X11/rgb FontPath unix/:7100 EndSection Section Module Load dbe Load extmod Load fbdevhw Load glx Load record Load freetype Load type1 Load dri EndSection Section InputDevice # Specify which keyboard LEDs can be user-controlled (eg, with xset(1)) # Option Xleds 1 2 3 # To disable the XKEYBOARD extension, uncomment XkbDisable. # Option XkbDisable # To customise the XKB settings to suit your keyboard, modify the # lines below (which are the defaults). For example, for a non-U.S. # keyboard, you will probably want to use: # Option XkbModel pc102 # If you have a US Microsoft Natural keyboard, you can use: # Option XkbModel microsoft # # Then to change the language, change the Layout setting. # For example, a german layout can be obtained with: # Option XkbLayout de # or: # Option XkbLayout de # Option XkbVariantnodeadkeys # # If you'd like to switch the positions of your capslock and # control keys, use: # Option XkbOptionsctrl:swapcaps # Or if you just want both to be control, use: # Option XkbOptionsctrl:nocaps # Identifier Keyboard0 Driver keyboard Option XkbModel pc105 Option XkbLayout fi EndSection Section InputDevice Identifier Mouse0 Driver mouse Option Protocol IMPS/2 Option Device /dev/input/mice Option ZAxisMapping 4 5 Option Emulate3Buttons yes EndSection Section Monitor Identifier Monitor0 VendorName Monitor Vendor ModelNameCPD-G520 DisplaySize 400300 HorizSync30.0 - 130.0 VertRefresh 48.0 - 170.0 Option dpms EndSection Section Device Identifier Videocard0 Driver radeon VendorName Videocard vendor BoardName ATI Radeon 8500LE EndSection Section Screen Identifier Screen0 Device Videocard0 MonitorMonitor0 DefaultDepth 24 DefaultDepth 24 SubSection Display Viewport 0 0 Depth 24 Modes1280x1024 1280x960 1152x864 1024x768 800x600 640x480 EndSubSection EndSection Section DRI Group0 Mode 0666 EndSection Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520???
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 sony G520 monitor , stereo graphics enabler cable and e2 emitter box. or am I flogging a dead horse cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] sony (sgi) monitorGDM-20D11 flashing LEDs, no picture
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 monitor blink together. I can use the machine via VNC from my Mac, so I can see it is running ok. any idea what the problem might be? I can't find the manual here, or any useful info on the internet just though someone might have seen this before...sometime.. cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2
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 pymol but on running build.com I got an error about previous declaration of memchr and sure enough there is a file on my system called /usr/include/string.h and line 69 has memchr is there a way around this? I edited build.com : setenv SGI_ABI -n32 setenv MAKE make setenv CXX /usr/freeware/bin/c++ are these ok? will the hardware stereo work with pymol? this is really all I need this machine for, good for students (unless I can get a new licensed version of insightII on it ... from the csc here in finland) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2
Hi, I restarted the installation from unix sources as released on pymol sourceforge page, made the appropriate changes to build.com in the ext directory and now it is compiling away quite happily so far, there must have been an error i introduced while I was trying to build with gcc 2.7 previously... anyway, with a clean source tree, i'm as far as tkWindow.c so far... still going cheers Dan On 16 Sep 2004, at 21:58, Warren DeLano wrote: Dan, It's been a decade or so since I've tried to install GCC on a system like that. It is always tricking getting the correct include paths to be used by the compiler. In this case, I think you're getting the IRIX includes when you really want the GCC includes, or vice versa, or your getting both confounded. Hardware stereo should work with PyMOL if and only if that Indy2 has hardware stereo support built in to the video option. I think the extreme does, but you may need to run in 1024x768 in order to enable it. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -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: 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 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 pymol but on running build.com I got an error about previous declaration of memchr and sure enough there is a file on my system called /usr/include/string.h and line 69 has memchr is there a way around this? I edited build.com : setenv SGI_ABI -n32 setenv MAKE make setenv CXX /usr/freeware/bin/c++ are these ok? will the hardware stereo work with pymol? this is really all I need this machine for, good for students (unless I can get a new licensed version of insightII on it ... from the csc here in finland) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi --- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2, external sources python build fails
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. -I./Include
-DPy_BUILD_CORE -o Python/thread.o Python/thread.c
/usr/include/sys/prctl.h, line 64: error(1020): identifier
k_sigset_t is
undefined
k_sigset_t t_hold; /* Hold signal bit mask */
^
1 error detected in the compilation of Python/thread.c.
*** Error code 2 (bu21)
*** Error code 1 (bu21)
rooster:/usr/people/dwhite/freestuff/pymolstuff/ext-0_95%
the relevant code from /usr/include/sys/prctl.h on the irix 6.2 system
is:
#define PRDA_PANCAKE_SIZE 5
/* the system portion of the prda */
struct prda_sys {
pid_t t_pid; /* epid */
__uint32_t t_hint; /* Share group scheduling hint */
__uint32_t t_dlactseq; /* Deadline scheduler activation seq# */
__uint32_t t_fpflags; /* Current p_fpflags (SMM, precise) */
__uint32_t t_prid; /* Processor type */
__uint32_t t_dlendseq; /* Deadline sched allocation seq # */
__uint64_t t_pancake[PRDA_PANCAKE_SIZE];/* registers for pancake */
pid_t t_rpid; /* pid */
__int32_t t_resched; /* send pthread resched signal */
__uint32_t t_unused[8];
/*
* The following field is used to hold the cpu number that the
* process is currently or last ran on
*/
__uint32_t t_cpu; /* Last/current cpu */
/*
* The following fields are used by sigprocmask if the hold mask is
* to be in user space.
*/
__uint32_t t_flags;/* t_hold mask is being used? */
k_sigset_t t_hold; /* Hold signal bit mask */
};
any clues anyone?
python2.1 for irix6.5 from sgi freeware won't install (of course, and
only python 1.5 is available for irix 6.3 on sgi freware)
cheers
Dan
Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology, Ambiotica C242
Department of biological and environmental science
PO Box 35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)
http://www.chalkie.org.uk
d...@chalkie.org.uk
wh...@cc.jyu.fi
[PyMOL] Re: hardware stereo in IRIX
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 desktop to pymol.com pymol version 0.97. then on menus bar Display-Stero mode- quad buffered. running at 1024x786_96s is display settings on SGI grey speckled monitor. Are all the cables connected properly for the emitter box? Dan On 23 Apr 2005, at 06:19, pymol-users-requ...@lists.sourceforge.net wrote: Hello PYMOLers, =20 I've recently installed Pymol v0.97 on an SGI but the hardware=20 stereo mode was not detected. Is there somebody successfully using PyMol=20 with this mode on an SGI ? If yes, could you please help me to fix this=20 problem? =20 My SGI: - Irix 64 Release 6.5 - Model Indigo 2 Impact 1 - Main Mem: 128 MB - CPU: 175 MHz =20 Thanks a lot, =20 Nicolas Ambert. --=20 Dr. Daniel James White BSc. (Hons.) PhD Bioimaging Coordinator Nanoscience Centre and Department of Biological and Environmental science Division of Molecular Recognition Ambiotica C242 PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
