- Chimera-dev - RBVI Mailing Lists

Re: [Chimera-users] compiling minrms on mac os10.2.8
by Eric Pettersen 02 Apr '04

02 Apr '04

On Friday, April 2, 2004, at 11:34 AM, Chris Adams wrote: > I am also trying to get minrms on my OS10.2.8 machine. I followed the > commands you recommended to Howard to get the "make" command to work. > However, my ls output was not at all like what you said would happen > in the message. I get this: > > ls -1 /usr/bin/*make > /usr/bin/automake One little thing is that you wanted to use the '-l' flag (lowercase L) rather than '-1' (numeral one). Nonetheless, either way this indicates that bsdmake and gnumake as well as the symbolic link from make to gnumake are missing. This indicates that the developer tools haven't been installed on your system. The developer tools came with your original installation CDs (on a separate CD) as an optional install. > and am unable to compile the minrms program. I am not very unix savvy > but am learning, perhaps you can help? You could install the developer tools and proceed from there. However, as part of the exchange with Howard I wound up compiling MinRMS myself and sending it to him. I will send you what I sent to him, but as a separate mail to avoid having the attachment sent to these lists. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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by Howard M. Fried 19 Mar '04

19 Mar '04

Hi: I'm trying to get MinRMS. I downloaded your source code but apparently my Mac with OS 10.2.8 does not have the 'make' program (I've got Developer Tools as well). My Unix-knowledgeable friend here confirmed this; he was unable to figure out how to compile MinRMS on my machine. As well, the computer support people here have been useless. Is there any way to obtain an executable version of MinRMS under X11 on Mac? Thanks, Howard Fried Dept. Biochemistry Univ. North Carolina-Chapel Hill

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Chimera on Athlon 64 / Linux
by Thomas Goddard 11 Mar '04

11 Mar '04

I compiled Chimera on an Athlon 64 processor running a 64 bit version of Linux for Steve Ludke using one of his machines. I had to fix about 20 build errors, mostly in foreign packages. There were 4 types of errors: 1) using /usr/X11R6/lib instead of /usr/X11R6/lib64 2) not using -fPIC compiler flag required for shared libraries 3) specifying -malign-double compiler option, illegal on this machine 4) g++ 3.3.1 bug related to throwing standard exceptions that generates "inconsistent operand constraints in an 'asm'". Work around by using -O2 or in some cases no -O# option I hand edited makefiles and configure scripts to make the compilation work. It took a full day. I didn't update our foreign build scripts. That would likely take a week. Since we don't have an Athlon 64 bit machine that doesn't seem worthwhile right now. Tom

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Fwd: ADC News #388
by Eric Pettersen 09 Mar '04

09 Mar '04

Kind of looks promising. --Eric Begin forwarded message: > HeaderDoc 8 Public Beta is a tool for generating HTML reference > documentation from comments in C, C++, and Objective-C header files. > It's written in Perl for easy portability. Similar to JavaDoc, it > allows developers to easily document their interfaces and export > that information into HTML. HeaderDoc 8 adds many new features, > including a new (optional) tagless syntax, code coloring, > template-based index pages, improved error checking, man page > output, and support for many new languages, including Java, > JavaScript, Perl, PHP shell scripts, and Pascal. > http://developer.apple.com/darwin/projects/headerdoc

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5 DOF JoyStick/Mouse
by Steve 26 Jan '04

26 Jan '04

I have recently received a patent on a new mouse that also acts like a joystick. Could I get some feedback from your team? Are you in the business of developing prototypes? Please check this out and let me know what you think about it. Feel free to share the info with anyone that might be interested. Please follow the following link to view the details. http://www.elegantsol.com Thanks, Steve Stephen Shaw 8 Eiker Road Cranbury NJ 08512 H 609 799 4574 W 908 956 2266 Cell 609 284 0316

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Chimera dead after NVidia driver install...
by Patrick Ladam 12 Jan '04

12 Jan '04

Hi all, I had chimera 1.1872 working OK on my MDK 9.2 Linux box until I installed the NVidia driver for my GeFOrce2 card. What happens now is that chimera launches but stops during start-up with an error box indicating this message: "Togl: Couldn't get visual" This sounds like an OpenGL problem to me but I am far from being a specialist on this. Does anyone have a clue how I can debug/fix this ? Bye -- -- ----------------------------------------------------------------- | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | e-mail: | | | ladam(a)smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | -----------------------------------------------------------------

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python 2.3
by Catherine.Lozupone＠colorado.edu 06 Jan '04

06 Jan '04

Hello, I was wondering when Chimera will be using python 2.3 and how one would go about integrating the current version of Chimera with python 2.3. Thanks, Cathy Lozupone

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Re: [chimera-dev] Problem using: "openModels.add"
by Lars Kunert 07 Dec '03

07 Dec '03

Hi! How do I set the transformation matrix by hand? (and how do I get it? ) >So until we get the next snapshot release out (should be soon), you >will need to specify shareXform=0 and set the transformation matrix "by >hand" if you need to. Thanks for your help, Lars

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Problem using: "openModels.add"
by Lars Kunert 04 Dec '03

04 Dec '03

Hi! I got a problem using openModel.add to add a model into a specified id/subid-slot. Python 2.2.3 (#1, Oct 29 2003, 07:35:58) [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2 Type "copyright", "credits" or "license" for more information. IDLE 0.8 -- press F1 for help >>> import chimera >>> m=chimera.Molecule() >>> chimera.openModels.add([m], baseId=0, subid=0 ) up till here it worked nicely... >>> m=chimera.Molecule() >>> chimera.openModels.add([m], baseId=0, subid=1 ) Traceback (most recent call last): File "<pyshell#4>", line 1, in ? chimera.openModels.add([m], baseId=0, subid=1 ) File "/usr/local/chimera/chimera-1.1872/share/chimera/__init__.py", line 769, in add shareXform, hidden, skipViewAll) error: unopen model adding a second, third... molecule/model to a slot gives an error-message (see above) - no new entry will show up in the model-viewer, but... >>> m=chimera.Molecule() the next created Model will be shown in the model-viewer without even being added. It would be nice if you could tell me something about the shareXform-parameter of the add-command too. Thanks a lot for your help, Lars

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Adding a button to my extension...
by Lars Kunert 25 Nov '03

25 Nov '03

Hi! My application (extension) works fine when execute it within the built-in IDLE. The python-code basically executes an external program (using "popen" ) and manages communication between the application and chimera through named pipes... (The external Application uses Qt and all my trials to smoothly integrate it by use of a python wrapper have failed...) Now I want to add an icon to chimera, which should call my extension in the same way I do it in the IDLE. I did not manage to get the ToolbarButtonPackage working: the related documentation seems to be completely outdated: ""The example code files and ToolbarButton.tiff must be saved in a directory named ToolbarButtonExtension. To run the example, start chimera, bring up the extension manager (via the Manager... entry in the Extensions menu), select the Directory tab, and Add the directory above the ToolbarButtonExtension directory. A MainChain entry should appear under the Utilities extension category."" Anyway, the ToolbarButtonExample works, but I can not adapt it to my application. When I add the path within the Favorites/Preferences/Tool - Tab chimera dies... I include the set of python files I use: Thanks for your help, Lars

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