Re: [PyMOL] (no subject)
Hi Blanton, Are you running the unstable tree, or have you just copied the pymol-0.90-2 package to stable, you either have to enable the unstable tree, or copy the numeric-py22 package from the unstable to stable, it can be found at '/sw/fink/dists/unstable/main/finkinfo/sci' see here; http://fink.sourceforge.net/faq/usage-fink.php#unstable Matt On Wednesday, Aug 20, 2003, at 12:01 Australia/Canberra, Tolbert, Blanton wrote: I was attempting to install pymol 0.9 using fink and got the following error message, Failed: Can't resolve dependency "numeric-py22" for package "pymol-0.90-2" (no matching packages/versions found) Can anyone advise me on what to do to get around this? Thanks in advance. Blanton --- This SF.net email is sponsored by Dice.com. Did you know that Dice has over 25,000 tech jobs available today? From careers in IT to Engineering to Tech Sales, Dice has tech jobs from the best hiring companies. http://www.dice.com/index.epl?rel_code=104 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] pymol fails to start
Is there a '/sw/lib/python2.2/lib-dynload/time.so' on your system? Matt On Sunday, Aug 17, 2003, at 20:23 Australia/Canberra, wkag...@jota.gsc.riken.go.jp wrote: The native and the x-windows version on mac fails to start. The following message appears in the terminal. Traceback (most recent call last): File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ? import threading File "/sw/lib/python2.2/threading.py", line 4, in ? import time ImportError: No module named time I've reinstalled pymol (0.86, 0.88, 0.90) and python2.2, but that did not resolve the problem. I have os 10.2.6. I appreciate any suggestions. Wataru Kagawa, Ph. D. Special Postdoctoral Researcher Protein Research Group RIKEN (Physical and Chemical Research Institute) W221, West Research Bldg. 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Japan 230-0045 tel.045-503-9206 fax.045-503-9201 --- 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/psa0013ave/ direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #354 - 3 msgs
Bill, Just discovered I had introduce a bug into the pymol package, now a new revision in cvs that fixes this. Matt On Sunday, Jul 6, 2003, at 08:21 Australia/Canberra, William Scott wrote: Hi Matt: I did it with fink. I'll try again next time I can escape to work. Thanks. Bill On Friday, July 4, 2003, at 09:26 PM, Matt Stephenson wrote: Bill, Did you build 0.90 manually using the 'Rules.osx-fink' makefile included in the pymol distribution, the 'Rules.osx-fink' makefile is slightly broken and won't work properly, just run 'fink selfupdate-cvs' and 'fink install pymol'. Matt On Friday, Jul 4, 2003, at 07:22 Australia/Canberra, wgsc...@chemistry.ucsc.edu wrote: When I installed X-windows pymol 0.90 on OS X using fink and try to run it, I get an error /sw/bin/python: can't open file '/Users/delwarl/pymol/modules/pymol/__init__.py' another user reported a different such error: /sw/lib/pymol/modules/pymol/__init__.py:300: RuntimeWarning: Python C API version mismatch for module _cmd: This Python has API version 1012, module _cmd has version 1011. import _cmd The OS X native version 0.9 works great by the way! -- scowilg William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) url: http://chemistry.ucsc.edu/scott_w.html
Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #354 - 3 msgs
Bill, Did you build 0.90 manually using the 'Rules.osx-fink' makefile included in the pymol distribution, the 'Rules.osx-fink' makefile is slightly broken and won't work properly, just run 'fink selfupdate-cvs' and 'fink install pymol'. Matt On Friday, Jul 4, 2003, at 07:22 Australia/Canberra, wgsc...@chemistry.ucsc.edu wrote: When I installed X-windows pymol 0.90 on OS X using fink and try to run it, I get an error /sw/bin/python: can't open file '/Users/delwarl/pymol/modules/pymol/__init__.py' another user reported a different such error: /sw/lib/pymol/modules/pymol/__init__.py:300: RuntimeWarning: Python C API version mismatch for module _cmd: This Python has API version 1012, module _cmd has version 1011. import _cmd The OS X native version 0.9 works great by the way! -- scowilg
Re: [PyMOL] Fink/pymol problem
On Wednesday, Apr 30, 2003, at 05:38 Australia/Sydney, Terry M. Gray wrote: Hi, Anybody know what this message is caused by? Yep :) I have seen this a couple times before, do you have a 'sw/lib/python2.2/lib-dynload/time.so' if you don't do a 'fink rebuild python22' even if it is there still do a 'fink rebuild python22' a rebuilding of python always seems to fix it. Matt [chem05:~] grayt% pymol Traceback (most recent call last): File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ? import threading File "/sw/lib/python2.2/threading.py", line 4, in ? import time ImportError: No module named time __
Re: [PyMOL] fink install of pymol
On Sunday, Apr 20, 2003, at 03:59 Australia/Sydney, Terry M. Gray wrote: In trying to install pymol 0.86-4 (I already have 0.86-1 installed), I was getting this this error: -- [chem05:~] grayt% fink install pymol sudo /sw/bin/fink install pymol Information about 2374 packages read in 3 seconds. Failed: Can't resolve dependency "python (= 2.2.2-4) | python-nox (= 2.2.2-3)" for package "pymol-0.86-4" (no matching packages/versions found) -- This was after I performed the steps given by Matt Stephenson in his email to the pymol list on 2003-03-18 13:02. I'm not a fink guru but it seems that pymol is looking for python 2.2.2-4 and can't find it since the version installed by fink is 2.2.2-6 (if you install python-2.2.2) or 2.3 something (if you install python). There has being a issue with python-2.3/python-2.2 and python modules in fink's unstable tree for the last 2-3 months. This has being fixed and you have just being caught in the 5-6 day time lag it took me to update the pymol package to reflect these new changes (was on holidays). If you run 'fink selfupdate-cvs' you will get a new revision of the pymol package which will work fine for you. So, I edited the pymol-0.86-4.info file and changed the dependency on python to = 2.2.2-5 and it seems to have compiled. I haven't tested all the features yet, but everything I check so far works. I'm sure this will wreck something unless the package maintainer just hasn't tested it thoroughly yet. I recommend not editing your package files as this can break your selfupdating, so before running 'fink selfupdate-cvs' delete the pymol-0.86-4.info. One thing that motivated me to try to update was the fact that I can't get surfaces or meshes to work right on my OS X machine (10.2.5, Apple's X11 beta 3) even with this newest pymol. After further trial and error it appears that surfaces work on proteins only when I use 1024 x 768 display resolution (not the wider 1152 x 768 that I normally use on my TiBook). Is this a known issue? Also, should I be able to create surfaces for non-protein atoms? Just so people know there is no difference in pymol itself between pymol-0.86-1 and pymol-0.86-5, the revision numbers are to deal with fink internals such as dependency issues. Also a note for the list, if your installing pymol via fink there is no need to enable the unstable tree pymol installs fine from stable, also haven't tried this yet but you should also now be able to do a full binary install of pymol through fink 'sudo apt-get install pymol'. Cheers Matt
Re: [PyMOL] compiling pymol --OS-X
On Friday, Mar 21, 2003, at 08:45 Australia/Sydney, Balaji Bhyravbhatla wrote: Hello All, I am new to the OS-X environment and would like some help getting the program running on a laptop. For practice I setup pymol on an older G3 and all went fine. Complete new install by me. Next I get a laptop of a student and I follow the same instructions of Bill Scott's but get a "Bus error" when the program is started from an xterm. The first time around immediate "Bus error" message. So then I do a "fink selfupdate-cvs" and a "fink update-all". No errors but this time around, a pymol window opens up before crashing with a "Bus error" Any help would be greatly appreciated. Thanks, please email me if you need further information (also how to get that info!!) What version of fink 'fink -V' and are you running stable or unstable tree. What version of OSX Matt
Re: [PyMOL] fink install fail: pymol-0.86-4
On Wednesday, Mar 19, 2003, at 07:42 Australia/Sydney, DeLano, Warren wrote: Kevin, It looks to me like you are missing Numeric Python. Either you need to remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy installed. There is likely a Fink package which contains it, but I suspect this dependency may have been missed in the creation of the Fink PyMOL package. No this is a problem in the fink unstable tree due to python-2.3 and numeric being install in the wrong spot. Cheers Matt
Re: [PyMOL] fink install fail: pymol-0.86-4
Do this, fink install python-2.2.2 fink rebuild numeric fink rebuild pmw fink install pymol Cheers Matt On Wednesday, Mar 19, 2003, at 05:58 Australia/Sydney, Kevin Gardner wrote: Hi all: I'll continue on a thread from a couple of weeks ago, re: failed fink-based installs of pymol over the past month or so. Here's the machine setup: - attempting to install pymol-0.86-4 onto OS 10.2.4 - python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs (2.2.4) all installed - running Apple's X11 (v0.2 and now 0.3) w/SDK installed, other X programs compiling OK Output from the build attached below --- anyone have any insights here? Thanks, Kevin -- cd pyopengl;make cc -ffast-math -no-cpp-precomp -g -I/sw/include -I/sw/include/python2.2 -I/usr/X11R6/include -D_HAVE_LIBPNG -D_PYMOL_MODULE -D_PYMOL_NUMPY -DHAVE_ARRAYOBJECT_H -c _glu_nummodule.c -DPythonTypes In file included from _glu_nummodule.c:8: _glumodule.c: In function `py_glu_NewTess': _glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type _glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from incompatible pointer type In file included from _glu_nummodule.c:8: _glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory _glumodule.c: In function `py_glu_Build2DMipmaps': _glumodule.c:723: `PyArrayObject' undeclared (first use in this function) _glumodule.c:723: (Each undeclared identifier is reported only once _glumodule.c:723: for each function it appears in.) _glumodule.c:723: `ap' undeclared (first use in this function) _glumodule.c:741: parse error before ')' token _glumodule.c:744: parse error before ')' token make[2]: *** [_glu_nummodule.o] Error 1 make[1]: *** [make-pyopengl] Error 2 make: *** [.contrib] Error 2 ### execution of make failed, exit code 2 Failed: compiling pymol-0.86-4 failed -- ** Kevin Gardner, Ph.D. kevin.gard...@utsouthwestern.edu Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center 214-648-8916/FAX: -8947 http://freedom7.swmed.edu --- This SF.net email is sponsored by: Does your code think in ink? You could win a Tablet PC. Get a free Tablet PC hat just for playing. What are you waiting for? http://ads.sourceforge.net/cgi-bin/redirect.pl?micr5043en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] failed fink installation of pymol-0.86-2
Also what version of python do you have installed??? 'fink list python' Matt Aki Hoji wrote: Dear, I tried to install pymol-0.86-2 by Fink but I got the failed compilation message as follows; make[2]: *** [_glu_nummodule.o] Error 1 make[1]: *** [make-pyopengl] Error 2 make: *** [.contrib] Error 2 ### execution of make failed, exit code 2 Failed: compiling pymol-0.86-2 failed I'd appreciate any help on fixing this. Thanks in advance. Aki Hoji Dept. Infectious Diseases & Microbiology University of Pittsburgh Rm526 Parran Hall, GSPH-IDM 130 Desoto St., Pittsburgh PA, 15261 tel: 412-624-3072 fax: 412-624-4953 --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] failed fink installation of pymol-0.86-2
Aki Hoji wrote: make[2]: *** [_glu_nummodule.o] Error 1 make[1]: *** [make-pyopengl] Error 2 make: *** [.contrib] Error 2 ### execution of make failed, exit code 2 Failed: compiling pymol-0.86-2 failed Need the output above this, this doesn't tell me enough, also are you running unstable??? Matt
Re: [PyMOL] Slow ray-tracing with PyMol 0.86 on OS 10.2.3/10.2.4
Povray was recently removed as dependency from the pymol package as it isn't really required to build and run pymol, so you probably don't have it installed, run 'fink install povray' and see if that helps. Matt On Saturday, Feb 22, 2003, at 06:56 Australia/Sydney, Hilgers, Mark wrote: I've installed PyMol 0.86 on multiple macs according to the instructions of Yuiwho/Bill Scott. It works beautifully except that identical ray tracings now take at least 10 times as long relative to the previous version, or to 0.86 on my PC (system specifics below). 1-2 minutes was a reasonable wait, but 30-40 minutes is just too long. There was mention on this mail list of Povray dependency failures, but at least as far as I can tell, nothing like this was an issue during installation. Has this been a problem for anyone else? Thanks, Mark Slow: Pymol 0.86 on 12" PowerBook G4 (867 MHz/640 MB RAM), OS 10.2.4 Pymol 0.86 on 15" PowerBook G3 (400 MHz/256 MB RAM), OS 10.2.3 Fast: Pymol 0.84 on 15" PowerBook G3 (400 MHz/256 MB RAM), OS 10.2.3 Pymol 0.86 on Dell PC (600 MHz/256 MB RAM), Windows 2000 Pymol 0.82 on 15" PowerBook G3 (400 MHz/256 MB RAM), OS 10.2.3 Mark Hilgers, Ph.D. Syrrx, Inc. 10410 Science Center Drive San Diego, CA 92121 Phone: (858) 731-3570 Mobile: (858) 442-0754 Fax: (858) 550-0526 E-mail: mark.hilg...@syrrx.com -- This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. --- This SF.net email is sponsored by: SlickEdit Inc. Develop an edge. The most comprehensive and flexible code editor you can use. Code faster. C/C++, C#, Java, HTML, XML, many more. FREE 30-Day Trial. www.slickedit.com/sourceforge ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Fink OSX version of PyMol 0.86 install - Help!
Do you have the developer tools installed??? Matt On Friday, Feb 21, 2003, at 13:05 Australia/Sydney, Jim Hu wrote: I'm a total UNIX newbie, so I have no idea of how to fix the following problem. Setup Powerbook G3 Pismo running OS10.2.4 HD partitioned into three partitions What I did: Downloaded and installed Apple X11 Downloaded and installed Fink Downloaded and installed Fink commander Note that for disk space reasons, I installed this onto a different drive partition than the one the has my OSX system Set Fink commander to use unstable packages Selected pymol Asked Fink commander to install it Accepted the default for several things it asked me for. I get the following error message: checking if --with-uniquename=NAME option specified... configure: error: No ar utility found. no checking for ar... missing_ar What do I do now? Thanks! Jim Hu --- This SF.net email is sponsored by: SlickEdit Inc. Develop an edge. The most comprehensive and flexible code editor you can use. Code faster. C/C++, C#, Java, HTML, XML, many more. FREE 30-Day Trial. www.slickedit.com/sourceforge ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] fink and povray
On Tuesday, Feb 4, 2003, at 09:14 Australia/Sydney, wgsc...@chemistry.ucsc.edu wrote: Regarding povray installation with fink: fink installs povray 3.5 without a problem for me. However, if you look at the file /sw/fink/10.2/stable/main/finkinfo/graphics/povray-3.50b-1.info you find the following dependencies: BuildDepends: libtiff, libjpeg, libpng, dlcompat-dev Depends: x11, libtiff-shlibs, libjpeg-shlibs, libpng-shlibs I am only guessing, but I think the problem you are having is with libpng. That shouldn't be a problem See the fink front page announcement: http://fink.sourceforge.net/ The problem apparently has arisen in the unstable branch of fink. Those who installed fink on 10.2 by the bootstrapping method a month or more ago probably are using the unstable branch. It might be a good idea to switch back to using the stable and cvs branches only. BTW, is there any reason for xwindows pymol to require that povray be installed? If not, we should email the maintainer and have that requirement removed. I was just deciding that myself, and will remove it as a dependency. Matt
Re: [PyMOL] pymol on OS X 10.2
Were you trying to install pymol via source or binary??? Matt On Tuesday, Feb 4, 2003, at 02:51 Australia/Sydney, Eugen Leitl wrote: I was trying to install PyMol using fink, but it fails the povray dependency. What is the best way to install? Compile from source? I have Apple's X11. --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
