December 2009 - Chimera-users - RBVI Mailing Lists

Movie spinning and slicing a density map
by Thomas Goddard 07 Dec '09

07 Dec '09

Hi Andy, I've added an example movie spinning and slicing a virus EM density map to the Chimera Animations page. See the bacteriophage phi6 entry. There is also a link to the movie script. http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom -------- Original Message -------- Subject: making a movie From: Anindito Sen To: Thomas Goddard Date: 12/2/09 5:50 PM > Hi Tom > > I am not sure if this email can be out on the general Chimera wiki. THe > following movie is from a published work of mine. Can you help me > getting the script for generating such a movie. There is a Chimera session in the > webpage but I think its a bit too much for me to understand. > > Please feel free to reframe the question and put it in the Chimera wiki > email list which may prove helpful to others. > > Thanks for your help. > > Best > > Andy > > > > http://emnavi.protein.osaka-u.ac.jp/emnavi_detail.php?id=1500 > > Dr. Anindito Sen (Ph.D) > >

2 1

drawing elipsolids
by Keren Lasker 04 Dec '09

04 Dec '09

Dear Chimera team, Is there a way to draw ellipsoids in Chimera. The ellipsoid is defined by its center and 3 radii. Thanks for your help. Best, Keren.

3 6

How to clip surface using mclip
by Marhoefer, R (Richard) 03 Dec '09

03 Dec '09

Dear Chimera Team and Users, I like to clip the surface of a model (but not the model itself) using the command mclip. Unfortunately, this command apparently is waiting for a model number and therefore works on the surface as well as the model itself. On the other hand, the interactive tool "Per Model Clipping" allows to clip the surface only. Because I like to use clipping in a movie, using the interactive interface is not an option. Does anybody know how this could be acomplished using the command line? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

3 2

Re: [Chimera-users] missing ribbon loop
by klumpler＠sci.muni.cz 03 Dec '09

03 Dec '09

Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas > Hello, > My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 27, 2009, at 2:16 AM, klumpler(a)sci.muni.cz wrote: > >> Hallo, >> please, can you tell me how to create missing part of ribbon >> representation of loop? >> >> Using "ball and stick" representation is peptide chain complete without >> gap, but in "ribbon" representation is one residue missing and forms the >> gap. >> >> Thank you very much >

2 2

keyboard input gone
by Zhou, Wei 03 Dec '09

03 Dec '09

Hi, Yesterday I installed the latest 1.4 32bit linux version of chimera into my opensuse 11.1. Soon after I fetched some pdb files and started to use it, at some point, I can no longer input any text into the program, such as typing another pdb id, or typing a command line, or type a file name to save it. I can still use mouse. Please help. I'm here at mission bay, rock hall. My extension is 60421. Thanks, Wei Zhou

2 1

phenix map not reading in chimera
by Geoffrey Feld 02 Dec '09

02 Dec '09

Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

3 2

Chimera question with Mac
by Durga Velukumar 01 Dec '09

01 Dec '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

5 6

Chimera-users December 2009