- Chimera-users - RBVI Mailing Lists

save image error in current daily build
by Ryan Pavlovicz 17 Mar '09

17 Mar '09

Hello, when trying to save an image with the current daily build of Chimera, i am finding that the program closes with the following error: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 10 (X_GLXCopyContext) Serial number of failed request: 0 Current serial number in output stream: 15993 Just wanted to let you know. Thanks, ryan

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Re: [Chimera-users] merge mrc volumes
by Anindito Sen 17 Mar '09

17 Mar '09

Hi Tom Carsten actually just took away my question. Thanks Carsten! It will be really helpful to have such feature ! Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Wed, 18/3/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] merge mrc volumes To: carsten.mim(a)yale.edu Cc: chimera-users(a)cgl.ucsf.edu Date: Wednesday, 18 March, 2009, 5:43 AM Hi Carsten, There's no facility in Chimera to combine (add) maps into a single map though it has been requested by many people and I am anxious to add such a command. Tom carsten.mim(a)yale.edu wrote: > Hi there, > I constructed a model with different .mrc files. Now I want to save the model as > a merged *.mrc file, containing all previous files. > > Thanks > > Carsten > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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merge mrc volumes
by carsten.mim＠yale.edu 17 Mar '09

17 Mar '09

Hi there, I constructed a model with different .mrc files. Now I want to save the model as a merged *.mrc file, containing all previous files. Thanks Carsten

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Changing default element colors
by Dipl.-Ing. Thomas Mitterfellner 17 Mar '09

17 Mar '09

Hello! Can the default element colors be changed easily and if so, how? Thank you, Tom

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Chimera
by taritkumar MITRA 17 Mar '09

17 Mar '09

Dear Sir, I have just installed windows version of Chimera. I am a retired Chemist taken up Molecular Modeling as a hobby. I have some experience of using Spartan and Hyperchem. I would very much like to use the Chimera specially for studies Docking. Are theire any publication or books which will help me in learning to use Chimera. I f so I would like to buy it. Can you please help? With regards Tarit taritmitra(a)hotmail.com

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DICOM maps
by triffo＠rice.edu 17 Mar '09

17 Mar '09

anyone out there know the easiest way to get a DICOM map (typical format for medical CT/MRI data; volume density map; .dcm file extension) into chimera? Is there a translator out there that will reformat DICOM data into a chimera-friendly volume map? thanks, -Jeff

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heme (fe) containing enzyme
by Agus Setiawan 17 Mar '09

17 Mar '09

Hi, I'm a student of Pharmacy and I just learn about chimera.Actually, I want to run a docking using Autodock so I have to minimze the structure of macromolecule first. I choose Chimera to minimize the structure of macromolecule. However, there is an error because the Fe atom doesn't have GAFF"Unable to find GAFF type for #0:500.A@FE"I also have a problem with hydrogen at Histidin residu"no MMTK name for H at standard HIS"How can Isolve this problem?I'll be very thankful for your answers.Best Regards, Agus Lee.

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Re: [Chimera-users] Making movies
by Elaine Meng 17 Mar '09

17 Mar '09

On Mar 16, 2009, at 10:13 PM, yimnai forlemu wrote: > Hello Elaine, > I have a quick question and was wondering whether I can use chimera > to archieve my goals.I have ran a BD simulation and saved > trajectories of my particles. My question is whether it is possible > for me to use chimera to create a movie from the BD simulations > trajectory data.If yes please could you just direct me to the > tutorial that can help me accomplish that goal. > Thanks > Neville Hi Neville, I don't know what "BD simulation" is. Chimera's "MD Movie" tool can read trajectory output from several programs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > If you have one of those formats, or can convert your output to one of those formats (for example, multiple PDB files), MD Movie can show the trajectory. You can control how the molecules look in Chimera as you normally do, then use "File... Record movie" from the MD Movie dialog to create a movie. This tutorial uses the MD Movie tool to do various things, including saving a movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > There are other ways to save a movie (not necessarily using the MD Movie tool). This page has more general information including links to example scripts and other movie-making tutorials: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine P.S. For a reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly. If you send mail to only me and I'm run over by a bus, you will never get an answer!

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Session management suggestions
by Thomas Goddard 16 Mar '09

16 Mar '09

Matt Dougherty sent 4 session file management suggestions. 1) Session description text, browsable. 2) Copying camera positions between sessions. 3) Session version numbers with matching filename extensions. 4) Automated checkpoint session saving. Details below. Tom Matthew Dougherty wrote: > 1) I frequently have to use a lot of session files in combination with a > lot of command files to generate animations. > > One session file might be used with multiple command files. > > I try to pack as much information into the filename as a way to keep it > all organized, but this is becoming cumbersome. > the filenames are becoming cryptic to keep them short; plus I multiple > drafts I need to maintain in case the researcher wants to go back to a > prior visualization. > > It would be good to have a item in the' File' pull-down-menu to handle > summaries or descriptions. > > By activating it, I could type in a paragraph as to what is going on > with the session. > > In a bigger picture, it would be good to be able to start chimera, and > somehow peruse through these descriptions, but not have to load the > session to read the description. > > 2) many times in an animation project I start with a common session file > containing all the data sets in sync, and create multiple derivative > session files to handle different aspects of the animation, usually with > the unused datasets deleted for a particular animation session for > reasons of improving computation speed and loading for a particular > animation clip. > > sometimes I would like to move a set of camera positions created in one > of the daughter session files to another daughter session file. > > Matthew Dougherty wrote: > 1) optional automated versioning. Sometimes I when I am working on an > animation I need to keep the intermediate versions, particularly when I > am less certain about what I am doing and the complexity of the session > goes up. > > check box somewhere that causes saving to automatically prepend "_V22" > before ".py", for version 22 in this example, and _V23 for the next > save, etc. > > 2) optional automated checkpoint saving such that the interval time can > be set. sometimes when working on a complex session it get a crash and > I have not saved it, so I have lost all my work from the previous save, > which could be 1-4 hours.

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Octamer to dimer
by John Lowenstein 16 Mar '09

16 Mar '09

Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks. Sincerely, John Lowenstein

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