[PyMOL] MacPyMOL in command line mode
Hello, I am trying to run MacPyMOL in command line mode with "-c -q" option. While directly logged in to the computer, it works. But if I ssh into the computer (even with X11 forwarding enabled), it fails with some errors about connecting to WindowServer And I can tell it actually tried to launch the GUI very briefly, then returned to the command line to process the scripts. Is this right? Can I run it remotely on another computer just from pure command line. Thanks. CY -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New MacBook
Yeah, my bad as I talked to Mark, hands faster than brain kind of thing :-), and in fact, we are getting a MacBook soon, I am going to try to see, and let everybody know. Chen On Fri, 19 May 2006, Serge Cohen wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Chen; I guess the question is not about getting a "universal binary", buth rather how the Radeon X1600 of the MacBook Pro compares with the GMA950 of the MacBook !!! Indeed I'd be very curious to know as well. Serge. Le 18 mai 06 à 20:40, Yu Chen a écrit : If you check the pymol website, the Feb 5th 2006 news announced MacPymol is now Universal Binary, and it rocks!!! We do have it running on MacBook Pros, realy fast! Chen On Thu, 18 May 2006, Mark A Saper wrote: I'm very interested in knowing whether PyMOL is usable on the new MacBook considering that it has Intel integrated graphics. Mark *** Serge Cohen GPG Key ID: 9CBB58FB *** -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (Darwin) iD8DBQFEbXQn5EPeG5y7WPsRAhE0AJ9+GWW8gvI/jGjCtEcoWmmnxlUEgQCg+Fug k2eL+faFyU+9pBnybzaExaw= =Csm8 -END PGP SIGNATURE- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] New MacBook
If you check the pymol website, the Feb 5th 2006 news announced MacPymol is now Universal Binary, and it rocks!!! We do have it running on MacBook Pros, realy fast! Chen On Thu, 18 May 2006, Mark A Saper wrote: I'm very interested in knowing whether PyMOL is usable on the new MacBook considering that it has Intel integrated graphics. Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: R: Re: [PyMOL] Linux NVidia segmentation fault
No, we don't have Quadro FX, we have 3DForce FX 5600-256. When we use the new drivers, it just sometime freeze the computers, not patically a Pymol related problem. Sorry couldn't help more, good luck. Chen On Tue, 12 Jul 2005, Paolo Tosco wrote: Thank you very much for your answer. Indeed I started experiencing the segmentation fault with driver 6629, which is the one shipped with RHEL 3.0. That's why I decided to try newer drivers. Is your graphic board a Nvidia Quadro FX? Maybe this issue doesn't come up with any Nvidia board, but only with some of them. I wonder if the problem is connected with the fact that I tried Pymol 0.98 and 0.99beta, but never 0.97. I will let you know if I will finally manage to solve the problem. Paolo === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] Linux NVidia segmentation fault
Have you tried 6629 driver? We also had some other problems with the newest driver, so we just switched back to 6629. On Tue, 12 Jul 2005, Paolo Tosco wrote: Hi everybody, I have read in the thread about the infamous "segmentation fault" issue concerning NVidia Linux drivers and PyMOL. Warren says that starting from release 7664 the problem has been solved, but I still experience the segmentation fault when working with medium sized proteins using surfaces. I tried the newest drivers 7667 and 7664 using both PyMOL 0.98 binary and PyMOL 0.99beta binary, and I had negative results. Then I even tried with drivers 7167 and 7174 which also should work with PyMOL 0.99beta, but I didn't manage to get rid of this segmentation fault. I'm running PyMOL on a RHEL 3.0 WS box with Kernel 2.4.21-9.EL (which is the one shipped with RHEL 3.0). I have read on the NVidia README file that this issue is connected with Kernels older than 2.6.x. But I can't upgrade my kernel, because I'm running other applications which require the original Kernel to work properly. When I work with the same protein under the same conditions on my Windows laptop (SiS 730 graphics card) PyMOL runs smoothly. Has anybody a suggestion how to manage running PyMOL with NVidia Quadro FX 1300/PCI/SSE2 under Linux without experiencing the segmentation fault after a few minutes? Thanks for your time Paolo Tosco ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] SOLUTION to nVidia driver problem
Just sharing our experience, we upgraded just before Warren's warning. Seems everything's fine so far. We are using RedHat Enterprise WS 3 (update 3) fully updated with kernel 2.4.21-27.0.2 on Intel(R) Xeon(TM) CPU 1700MHz with 512MB mem Regards, Chen On Fri, 22 Apr 2005, Peter Dudek wrote: Hello everyone, I found a temporary solution to the driver problem, in case there are people out there who are too lazy to roll them back (like me). Basically, when running pymol from the command-line with the new drivers, an error regarding the TLS library is produced: ImportError: libnvidia-tls.so.1: cannot handle TLS data This was the exact same error I was getting after installing the 6111 drivers for the first time - but at the time, it seemed I was the only one on this list with this problem (you can scan the archive for the thread). However, the solution remains the same. Renaming /usr/lib/tls to something else (/usr/lib/tls_backup) for instance, solved this issue. Now pymol launches and is accelerated normally. I'm running Debian SID, kernel 2.4.26, on AMD64 hardware. Regards, Peter -- Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Sciences III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@cellbio.unige.ch http://www.picard.ch/DP/DPhome.html --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] pymol crashes with very large structures?
I did it on RedHat EL-AS-3, Intel 1.7GHz, single cpu, 512MB memory,
GeForceFX 5600 (256MB Mem on chip) without problem, it took about 5-6 mins
to load with the same commands as Douglas has run.
Chen
On Sun, 9 Jan 2005, Douglas Kojetin wrote:
I didn't keep track of how long it took (and it took a while), but I was able
to successfully run the following commands under OS X using MacPymol 0.95 on
a machine w/ 1.5GB RAM.
load 1JJ2.pdb
hide all
show surface
Doug
On Jan 9, 2005, at 1:45 PM, Wulf Dirk Leuschner wrote:
I use an AMD 2 GHz machine with 1 GB of RAM (recently added 512 MB) with a
GeForce5200 graphics card, and I was quite happy with the performance
(Windows - Linux is currently not possible since the machine I got Linux
installed on is too slow) for the 65,000 atoms of the smaller ribosome
structure. Surface rendering of that structure takes about 2.5 min with an
initial memory usage of about 1.25 GB.
With respect to the crash with 1JJ2.pdb: pymol shuts down immediately - no
pymol processes running anymore.
Warren proposed to set the surface mode to -1 or -2, but I got the same
result: it crashed again.
After that I thought maybe my new memory is faulty and ran an exhaustive
memory check - without any errors.
I then selected chain A of the structure and then used 'show surface,a'
('a'
being the selected protein chain): this worked fine! Three chains: fine!
All
atoms: crash!
I wonder if anybody with a 'decent' machine could try the same and let me
know if they got the same problem. If not, it's my machine and I won't
bother anybody anymore ;-)
Thanks in advance!
WDL
Here's the direct link to the PDB entry:
http://www.rcsb.org/pdb/cgi/explore.cgi?
job=download&pdbId=1JJ2&page=&pid=282541105295401
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===
Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 182
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250
phone: (410)455-6347 (primary)
(410)455-2718 (secondary)
fax:(410)455-1174
email: c...@hhmi.umbc.edu
===
Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
Hi, Peter What Linux are you using? Seems it's not a problem on RedHat linux, I am running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel respectively, and the exact same NVIDIA version without any problem at all. Although we are using python2.2, looks like you are using python2.3, maybe that's the problem? Best Chen On Wed, 13 Oct 2004 peter.du...@cellbio.unige.ch wrote: Hello. I did a scan (albeit brief) of the mailing list for this issue, but didn't find it, so I decided to post it FYI. I wanted to mention a serious issue I just discovered after installing the new nvidia drivers for linux (specifically regarding the "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the same is true for all other 6111 drivers), on a 2.4.x kernel, as well as the solution. It may be important to make a note of this somewhere in the FAQ or installation instructions (or perhaps it would be easy to fix in one of the pymol scripts). PROBLEM: Running Pymol gives the following message: Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 90, in ? import pymol File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 306, in ? import _cmd ImportError: libnvidia-tls.so.1: cannot handle TLS data SOLUTIONS: == There are 2 solutions to this problem. (1) either rename /usr/lib/tls to something else, or delete it entirely. Pymol then works perfectly ok. However, since this is akin to "If it hurts, cut it off", it might break something down the line. Do note though, that the files contained within this dir are also in /usr/lib (not a symbolic link). (2) edit /etc/default/nvidia-glx (if it exists, for me it didn't), and set USE_TLS to 0. Reboot. Surely there must be another editable config file somewhere with this option, but I haven't found it. According to a thread on PyKDE, "The tls (thread local storage) stuff only works if you are running a tls-enabled glibc on a 2.6 kernel, and when installing nvidia-glx, you are normally asked by debconf on what to use." This suggests anyone running the new nvidia drivers on a 2.4.x kernel may encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, so I can't be sure the problem doesn't occur there either. Hope this helps someone. Cheers, Peter _.--'"`'--.__.--'"`'--.__.--'"`'--.__ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' ` Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Scinces III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@cellbio.unige.ch http://www.picard.ch/DP/DPhome.html _.--'"`'--.__.--'"`'--.__.--'"`'--.__ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' ` --- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] graphics with GeForce4 card in windows vs. linux
You will need to download linux driver for GeForce 4 and install it under linux. The linux is not using the 3D-hardware accelaration without the manufacture's driver. On Tue, 14 Sep 2004, Eric Schreiter wrote: > Hi All, > I have a machine running WindowsXP and RedHat 9 with an Albatron GeForce > 4 Ti4800se graphics card. I notice that when I run pymol in windows it > is much faster and smoother than when I run in linux. When I open PyMol > in windows, it says "Adapting to GeForce hardware..." but does not say > this when I open it in linux. Any thoughts on how I can get pymol to > run more smoothly in linux? Thanks for your help. > Cheers, > Eric > > > > --- > This SF.Net email is sponsored by: thawte's Crypto Challenge Vl > Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam > Camcorder. More prizes in the weekly Lunch Hour Challenge. > Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] PyMOL 0.96 Released
Hi, just wondering if this is a bug or just my system. I was just exploring the new PyMOL, there is a menu item "plugin", when I clicked the pull-down menu "about plugins", PyMOL quit, gives out segmentation fault error. Thanks! Chen -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
RE: [PyMOL] electrostatic
PyMOL takes care of this, thanks again Warren! > > Are you using the same platform for both Grasp and Pymol? I don't think > that big-endian maps (written by an SGI computer) can be read by a > little-endian platform, such as a x86 based PC. ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] electrostatic
> I have tried getting the electrostatic in pymol using the following commands: > load molecule.pdb, mol-object > load grasp-map.phi, map-object > ramp_new ramp-name, map-object > show surface, mol-object > set surface_color, ramp-name, mol-object > The problem is getting the phi map in grasp. Can somebody explain me how to > do it? > This is what we did and worked (we now using Delphi), try it. -- *On the SGI computers: 1) Start up the computer, log in and in a command line prompt, change the directory to where the .pdb fi le, .siz file and .crg files are located. 2) Run grasp (command: /hhmi/software/grasp/grasp) 3) Open up the menu by right-clicking on the window 4) With the menu open, right-click on the Read option. 5) Right-click on the PDB File option and load the .pdb file. 6) Open the read menu again (steps 3-4), and select the Radius/Charge File option, then load the raidus file. Repeat again, loading the charge file. 7) Open the main menu, click on display, show, molecular surface. 8) Open the main menu, click on calculate, new potential map. 9) Open the main menu, click on calculate, Pot. via map at surface/atoms 10) Open the main menu, click on write, potential map, internal map, let me enter it. In the command lin e prompt, type in the name of the file (namefile.phi) ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (primary) (410)455-2718 (secondary) fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] graphics boards
Yes, Nvidia card is the best for Linux. I've tried Matrox, ATI, nvidia. Only the nvidia worked for us since we have dual monitor setup. If you only work with single monitor, the ati works fine too. The driver installation is simple and easy, and they are much linux friendly than others. Chen On Tue, 20 Apr 2004, Ezequiel Panepucci wrote: > Mark, > > You can get an Nvidia Quadro4 380 XGL which has a stereo connector. > > Nvidia keeps their drivers on almost the same (if not the same) > release schedule as their MS Windows drivers, they are very stable and > easy to install and maintain. > > Zac > > | I know this has been discussed before on this list. I need a graphics > | board for a Linux RH 9.0 running on Dell Optiplex GX270. The > | applications will be O and Pymol and similar programs. Stereo-capable > | would be preferred. I've been told that NVidia is more compatible with > | Linux. Of the myriad of models available, could anyone help narrow the > | choices for me? Price range <$150. > > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] installation problem
The warning is ok, just ignore. And to check the rpm package, use "pymol" as package name, not with version numbers. like 'rpm -q pymol' Chen On Thu, 15 Apr 2004, Shu-Hsien Sheu wrote: > Hi, > > Our system administrator of a linux cluster have trouble upgrading from 0.93 > to 0.95: > > [mfitz...@man local]$ sudo rpm -U --test pymol-0.95-1.rh73.py22.i386.rpm > [mfitz...@man local]$ sudo rpm -U pymol-0.95-1.rh73.py22.i386.rpm > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not > installed > > Any ideas? > > Thanks! > shuhsien > > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Marc Saric > Sent: Thursday, April 15, 2004 8:15 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] spectrum > > Hi all, > > I have a question regarding the spectrum command and b-factors. How are > the color-ranges calculated by "spectrum"? > > I.e. i would like to know the values for the different shades like in > the color_b.py-script, which gives you not only a total range, but also > the bins. > > I would like to put a color-gradient-bar below a picture which shows > numbers as well, and for that I need to know the ranges of blue, green, > yellow, etc. > > Or is it possible to do this from within Pymol automatically (like for > iso-surfaces)? > > Thanks in advance. > > -- > Bye, > Marc Saric > > > --- > 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_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > --- > 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_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Re: Need advice on graphic card
I just tried Summit Xserver, it is definitly a looot fast. But ... in single head mode. They claim they support Matrox Millennium G450 multihead. In dual view 1600x1200 mode, the pymol won't lanuch, gave out: GLUT: fatal error in pymol, visual with neccessary capbilities not found. But in dual view 1152x864 and under, it does lauch, but not as fast as in single head mode, and some of the screen goes out of the monitor. And the price for the Summit multi-head is more than the price for a new good graphic card. I just have ordered ATI radeon 9600 PRO and 9600, will see how it goes. Thanks for the informations. Chen > 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 2003, at 06:25, pymol-users-requ...@lists.sourceforge.net > wrote: > > > --__--__-- > > > > Message: 3 > > Date: Tue, 11 Nov 2003 12:17:20 -0500 (EST) > > From: Yu Chen > > To: Marc Saric > > cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Need advice on graphic card > > > > the "merged mode" is just one framebuffer for both display, so fool the > > system thinking it's only a "single-head" presented. > > No, Xinerama won't work with DRI. That's why i used merged mode, but it > > messed up nmrview's font. > > > > Seems nobody else out there using two screens? > > > > Thanks anyway, Marc > > Chen > 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 sponsored by: ApacheCon 2003, > 16-19 November in Las Vegas. Learn firsthand the latest > developments in Apache, PHP, Perl, XML, Java, MySQL, > WebDAV, and more! http://www.apachecon.com/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
Re: [PyMOL] Need advice on graphic card
the "merged mode" is just one framebuffer for both display, so fool the system thinking it's only a "single-head" presented. No, Xinerama won't work with DRI. That's why i used merged mode, but it messed up nmrview's font. Seems nobody else out there using two screens? Thanks anyway, Marc Chen > > What does "merged mode" mean? > > I know that most XFree86 drivers do not support OpenGL-3D-acceleration > when used in Cinerama-mode (i.e. dual-head with one continuous desktop). > > As far as I know, nVidia claims, that their driver can do that though > (but I haven't tested it, due to lack of a second screen and a dual-head > graphics-card. > > -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
[PyMOL] Need advice on graphic card
Hello, pymolers I checked pymol's homepage about the graphic card. But still not so sure, hope someone would have similar setting as ours, so could give us some advices on what card to buy. We running Redhat 7.3, XFree86 4.2.0, kernel 2.4.18-3. Currently, we running on Matrox Millennium G450, the 3D-accelleration works fine in Merged mode but not in dual-head mode. While nmrview works fine in dual-head mode, but font messed up in Merged mode. So we can't get both to work right at the same setting. So will Radeon 8500 work with both? Thanks in advance for your advice! Best Chen -- ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
RE: [PyMOL] Electrostatic potential maps in PyMOL
Thanks everybody for suggestiones, and Warren for fixing the problem. I will see if we could generate some phimap not 65x65x65. Ksushik, I don't know why your Delphi is working fine, here is my output from load phimap, which it should be cause of the endianess: PHIMapToStr: now starting phimap PHIMapToStr: potential PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine PHIMapToStr: j# ObjectMap: Map Read. Range = -3388. to 37 Crystal: Unit Cell1.0001.0001.000 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: FracToReal Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: Unit Cell Volume1. Executive: object "map" created. Best Yu ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu === On Wed, 9 Jul 2003, Warren L. DeLano wrote: > Okay, scratch that -- I fixed the problem, relying on "standard" > Fortran unformatted IO conventions to automatically determine endianness > and map size. > > PyMOL should now be able to read a PHI map of any dimensionality, so > long as record size is implicitly and correctly specified in the map > file. This may or may not be the case for ".phi" files written from C > (for example, "fld2phi" is hard-coded for a 65x65x65 map, because the > data block's record length specifier is hardcoded to be 0x10c304 = > 65*65*65*4). > > Can someone send me a PHI map which is not 65x65x65 for testing > purposes? Please include the associated PDB file for visual > verification. Thanks! > > Looks like we'll need to push out another release sooner rather than > later... > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.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 Warren L. DeLano > > Sent: Wednesday, July 09, 2003 2:20 PM > > To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' > > Cc: pymol-users@lists.sourceforge.net > > Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL > > > > Yes, you have identified the problem: PyMOL 0.90 currently only reads > > PHI files in one of the two endian formats (not sure if it is big or > > little). > > > > The problem is, how it PyMOL to determine which format the incoming > map > > is in? The file format is so darn implicit, I haven't yet come up > with > > any effective way of doing it without risking a floating exception on > > finicky hardware. > > > > Any ideas? If we can just determine the "enddian-ness" of the > incoming > > file, then the rest is a snap. > > > > Warren > > > > -- > > mailto:war...@delanoscientific.com > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax (650)-593-4020 > > > > > > > > > > > > --- > > This SF.Net email sponsored by: Parasoft > > Error proof Web apps, automate testing & more. > > Download & eval WebKing and get a free book. > > www.parasoft.com/bulletproofapps > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
Re: [PyMOL] Electrostatic potential maps in PyMOL
Hello, Kaushik Yeah, we do had problems with DelPhi to PyMoL. I don't know what your mean by "modified version of Delphi..." We bought the latest Delphi from their website, and used the data from all the example folders comes with Delphi. The calculation all went well. When we tried to read the phimap into PyMoL, after load delphi-map.phi, e_pot In the console window, the line objectMap: Map Read. Range= -... to .. Then range is incredibly large, the negtive and positive values each has about over 30 digits! But when we use the same data in GRASP to generate the phimap, it reads in well. If you could give us some advice on how you modified Delphi, or how to get it, we would be greatly appreciate! Best Yu Chen ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 email: c...@hhmi.umbc.edu === On Wed, 9 Jul 2003, Kaushik Raha wrote: > There has been some talk on the list regarding failure of PyMOL in > reading Delphi generated potential maps that I missed. I have generated > phimap using a modified version of Delphi in the GRASP format that > PyMOL reads and displays without any problem. So I am not sure what the > problem is. Can anybody please let me know what was the problem with > PyMOL reading Delphi generated GRASP potential maps? Was wondering if > PyMOL is doing the right thing?? > > Thanks, > Kaushik Raha > Penn State University > > On Wednesday, July 9, 2003, at 10:48 AM, EPF (Esben Peter Friis) wrote: > > > > > Hi PyMOL users, > > > > MEAD's potential maps can be used in PyMOL, but it requires a little > > more > > than a bit of tweaking, as the maps are in the AVS .fld format, which > > can > > not be read by PyMOL. (These maps can be read by Dino, as Paulo just > > mentioned). Also, PyMOL reads (as far as I can see) only big-endian > > phi-maps. > > > > I have written a small program, which does the conversion from .fld to > > big-endian-.phi, so the maps can be read by PyMOL. It just finished it > > today, and it has only been tested on Linux (i386), so beware ;-) > > > > To create a nice electrostatic surface, you need: > > > > > > * Gromacs (not strictly necessary, but makes life easier) Download from > > http://www.gromacs.org > > * MEAD. Download from http://www.scripps.edu/bashford/ > > * fld2phi, source code quoted below (sorry, but I don't have access to > > our > > external web server, and it's only about 4kb). > > * PyMOL, of course (v0.88 or newer). > > > > > > Here is an example how to create everything from scratch for 4PTI.pdb > > > > > > Gromacs steps > > - > > 1) use pdb2gmx to create .gro and .top files: > > pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top > > > > 2) use grompp to create .tpr file: > > grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro > > > > The file 4PTI.mdp contains the parameters for the Gromacs simulation. > > But as > > we are not going to do any simulation this time, an empty file is ok. > > It can > > be created with touch 4PTI.mdp. > > > > 3) use editconf to create a MEAD-readable pdb file: > > editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb > > > > The output pdb file must then be renamed to be recognized by MEAD: > > mv 4PTI.pqr.pdb 4PTI.pqr > > > > > > MEAD steps > > -- > > > > 1) create a .ogm file which specifies the grid size. Notice that PyMOL > > can > > only handle grids which are 65x65x65 points, so your only option is to > > change the spacing between points. You can specify focussing options > > in the > > .ogm file, but only the coarsest grid is written anyway, so you only > > need > > one line in the 4PTI.ogm file: > > > > ON_GEOM_CENT 65 1.0 > > > > See documentation for other centering options (first parameter). Next > > number > > is the number of grid points on each side (must be 65 to be readable by > > PyMOL). The last number is a real specifying the distance between grid > > points. > > > > 2) Run 'potential' to create the grid: > > potential -epsin 2 -CoarseFieldOut 4PTI 4PTI > > > > The epsin option is mandatory and specifies the internal (in the > > protein) > > dielectric constant. The program will say something like: > > > > WARINING from potential main program: > > Could not open field point file, 4PTI.fpt, for reading. Exiting without > > giving any pote
RE: [PyMOL] can't initialize module sglite
Thanks, Warren I think it's the Python problem, i will try it. On Mon, 7 Jul 2003, Warren L. DeLano wrote: > Yu Chen, > > There are two likely causes of this problem: > > (1) An old pymol.com file > > This may be caused by use of an outdated "pymol.com" startup > script. The launch requirements for PyMOL changed slightly in this new > version, so it may be necessary to create a fresh "pymol.com" from one > of the templates in the setup directory. > > (2) Linking against Python 1.52 > > Make sure that Python is linking against version 2.x if > possible. If you must use 1.52, you will need to compile the older > versions of ExtensionClass.c and ExtensionClass.h located in the > contrib/modules directory. > > I hope this helps. > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.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 Yu Chen > > Sent: Monday, July 07, 2003 12:34 PM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] can't initialize module sglite > > > > Hello, pymolers > > > > I installed pymol-0.90 from tar file on Redhat Linux 7.2 the same way > as I > > installed pymol-0.88, the compiling all went well. But when running > pymol, > > it gives out: > > Fatal error: can't initialize module sglite > > > > Not sure what happened, any help would be appreciated! > > > > Thanks in advance! > > Yu > > > > > > === > > Yu Chen > > Howard Hughes Medical Institute > > Chemistry Building, Rm 122 > > University of Maryland at Baltimore County > > 1000 Hilltop Circle > > Baltimore, MD 21250 > > > > phone: (410)455-6347 > > (410)455-2718 > > fax:(410)455-1174 > > email: c...@hhmi.umbc.edu > > === > > > > > > > > --- > > This SF.Net email sponsored by: Free pre-built ASP.NET sites including > > Data Reports, E-commerce, Portals, and Forums are available now. > > Download today and enter to win an XBOX or Visual Studio .NET. > > > http://aspnet.click-url.com/go/psa0016ave/direct;at.asp_061203_01/01 > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
[PyMOL] can't initialize module sglite
Hello, pymolers I installed pymol-0.90 from tar file on Redhat Linux 7.2 the same way as I installed pymol-0.88, the compiling all went well. But when running pymol, it gives out: Fatal error: can't initialize module sglite Not sure what happened, any help would be appreciated! Thanks in advance! Yu ======= Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
[PyMOL] Emulate 3-button mouse in pymol
Hi, I installed pymol on MAC G4 laptop, since it only has a 1-button touch pad, how do I emulate a 3-button mouse using some keys combined with the one button, juse like under Xdarwin I can configure it with option+click and command+click. Thanks! === Yu Chen Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 fax: (410)455-1174 email: c...@hhmi.umbc.edu ===
