October 2006 - Chimera-users - RBVI Mailing Lists

Chimera under FreeBSD
by Devon Ryan 01 Nov '06

01 Nov '06

Has anyone had success getting chimera to run under FreeBSD? I can get the linux version to start (under the linuxulator), but it crashes after ~20 seconds when the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel architecture. Thanks -- Devon Ryan | dpryan(a)sg.uchicago.edu Neuro Grad Student, Ptacek Lab | dpryan(a)phy.ucsf.edu University of Chicago '02 | dpryan(a)alumni.uchicago.edu www.dpryan.com | dpryan(a)dpryan.com ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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question regarding chimera 1.2304-wim32.exe
by AJ Campbell 31 Oct '06

31 Oct '06

I have tried installing Chimera several times on my Windows machine but keep receiving an error message saying "Outline highlight not supported by hardware", any advice would be appreciated. ~ Arthur

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atom name balloons
by Greg Pintilie 31 Oct '06

31 Oct '06

I was wondering why in the new release of Chimera ballons no longer pop up when the mouse is placed over an atom and is left there... is this an option that has to be set somewhere? I found it extremely usefull and now am missing it... Greg

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problems with starting Chimera
by Mareike Goeritz 30 Oct '06

30 Oct '06

Hello, I'm interested in using Chimera, but after downloading and installing the software I'm unable to launch the program. I always get the following error message: "Microsoft Visual C++ Runtime Library: Assertion failed! Program: C:\Program Files\Chimera\bin\pythonw.exe File: togl.c Line: 2994 Expression: res==TRUE For information on how your program can cause an assertion failure, see the Visual C++ documentation on asserts (Press Retry to debug the application - JIT must be enabled)" I'm not familiar with C++, so I don't know what to do. Does anybody know what might be missing or what's the problem? Thank you for your help!! Mareike -- ******************************** Dr. Mareike Goeritz Department of Chemistry, MC 164-30 California Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 (626) 395-6032 Tel (626) 683-8753 Fax goeritz(a)caltech.edu ********************************

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Chimera, 3dsmax, blender
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Lydia, It's been years since I've had access to a 3dsmax license, so I can't really make good comparisons between it and Blender. Fundamentally, they serve the same role, so I expect you would find using them similar, especially compared to PyMOL, Chimera, etc. Before getting into the benefits, you should be aware that compared to any software truly designed for chemical modeling, Blender has some serious drawbacks. There is no pre-existing set of structural tools that is standard for chemistry modeling software: if you want ribbons, you have to write a procedure that will generate them. I'm assuming you're already familiar with this, though, since you're using 3dsmax. As another sizeable negative, CSG in Blender is still somewhat flaky. I seem to remember having far fewer problems in 3d studio, even back around ~R5 or 6. On the benefit side, Blender's plugin/scripting system is extremely free of restrictions. The scripting system is pure Python, and many Python "plugins" are available. The true plugins are done in C, but are currently restricted to some post-processing features. You could also use the scripting system to access C libraries. These features really help to make up for the lack of built-in chemistry-centered tools. The other reason why you might prefer Blender over 3dsmax is that the scripting and plugin system is very much like Chimera, so if you're using both it's only one system to learn. Jonathan > Message: 8 > Date: Mon, 30 Oct 2006 14:47:06 -0800 > From: "Lydia Jablonski" <lydka(a)uoregon.edu> > Subject: [Chimera-users] Exporting VRML, Using Blender > > Jonathan and Greg- > > Thank you for your suggestions. I wanted to at least try them before I responded. > > Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible. > > Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up. > > Any more pointers would be much appreciated. > > -Lydia

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Toolbar and Favorite on PC
by jean-francois menetret 30 Oct '06

30 Oct '06

Hello all, when running chimera on my PC (windows XP), my toolbar stopped being displayed. If I uninstall and reinstall chimera, my toolbar comes back until the next reboot. How can I fix that ? Is there to restore my preferences after launching chimera? Regards Jean-Francois Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although this does not relate to your question on licensing, is there any particular reason you're using such a complicated workflow? Chimera can be used to generate basic geometry (sphere/cylinder) from PDB files via povray, but so could any import system you have for the 3D modeling software. You would also lose the benefit of chemistry-centered structure for manipulation or selection: chains, residues, etc. I've been using Blender to handle complicated chemical models for a while now, and it wasn't that difficult to implement the import of various data types. With BioPython pdb files become trivial, and volumetric data sets are (very) difficult but possible. Jonathan > Hello- > > Do any of you have an idea of how much a single commercial license for Chimera would cost? > > I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max. > > Thanks, > > Lydia Jablonski

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changing center of rotation
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although I haven't used EMAnimator, you can set the center of rotation within Chimera using the Set Pivot action: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot There's also Tools/Movement/Rotation, and lastly, you can edit structures to insert artificial points at extreme high/low XYZ locations, which will in effect manually set the center used via the 'center of models' option. I wouldn't recommend the last option unless you have a good reason to do so, but it does work. Jonathan > Message: 1 > Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST) > From: wendy ochoa <wencryo(a)yahoo.com> > Subject: [Chimera-users] rotating molecules for movies > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <20061030195242.57847.qmail(a)web37306.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? > Thanks > > > >

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Re: [Chimera-users] viewing grid density
by Thomas Goddard 30 Oct '06

30 Oct '06

Bala reports that the problem was in an Amber input file. > From: "bala" <bala(a)igib.res.in> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] viewing grid density > Date: Fri, 27 Oct 2006 19:59:38 +0530 > > Hello Thomas and Elaine, > > Thank you for your information. I rechecked the amber input files and i = > found a mistake there in rms fitting the coordinates in my trajectory. > > regards, > Bala

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Re: [Chimera-users] rotating molecules for movies
by Thomas Goddard 30 Oct '06

30 Oct '06

Hi Wendy, Here are some Chimera commands that are useful for making movies with Movie Recorder: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Here's a fancier Chimera movie script example. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com Here is the documentation for the Movie Recorder dialog and movie command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom

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Chimera-users October 2006