[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: 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 thisnbsp;issue doesn'tnbsp;come upnbsp;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 letnbsp;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] 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=downloadpdbId=1JJ2page=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] 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] 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=1470alloc_id=3638op=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=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[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 potentials. This can be ignored. The program still writes out a 4PTI.fld file with the grid. Notice that this file in not overwritten, so you must delete it manually if it already exists. Convert to PyMOL readable grid -- 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: fld2phi 4PTI.fld 4PTI.phi This sould create a 4PTI.phi file which is readable by PyMOL. PyMOL steps --- 1) Load the structure including the hydrogens built by Gromacs: load 4PTI.pqr, 4PTI 2) Create a selection of the water: select water, 4PTI and resn SOL 3) Remove the water atoms: remove water 4) Show the surface of the 4PTI object: show surface, 4PTI 5
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
