- Chimera-users - RBVI Mailing Lists

Problems open Amber trajectory
by Koch, O (Oliver) 19 Aug '09

19 Aug '09

Dear Chimera Team, I have a problem opening an AMBER trajectory using chimera v1.3 (2000/12/09). When I look at the frames, they show this "spider web" phenomenon: Connections between atoms that should not be there. Furthermore, I got errors throughout the whole file: "Error: line too long in:" I have a topology file and a coordinate file created using leap/ptraj from the Amber Tools 1.2. I could look at the files using vmd with the options "Amber 7 parm" for the topology file and "Amber coordinates with periodic box" for the coordinate file. Therefore, the files should not be corrupt, but, of course, I would prefer to use Chimera for visualizing... Can you give me any advice how to open the files correctly? Thanks in advance. Kind regards, Oliver Dr. Oliver Koch BioChemInformatics Postdoctoral-Fellow Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: oliver.koch(a)sp.intervet.com Phone: +49 (6130) 948 396 Fax: +49 (6130) 948 517 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. --------------------------------------

2 1

erase octant question
by Kristin Parent 18 Aug '09

18 Aug '09

Hello, I was wondering if you could help me. I am trying to visualize a 3D density map from a cryo-TEM reconstruction of a virus (ccp4 format). I would like to use the "erase octant" function (link below), but actually erase a full quarter of the map to see inside the interior. I would like to do it accurately, and not by dragging the subregions box by hand. Can you help me understand how to set the command line function in order to do this? Thanks in advance. Kristin http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

2 2

Re: [Chimera-users] Chimera frame storage director
by Elaine Meng 14 Aug '09

14 Aug '09

On Aug 14, 2009, at 12:34 PM, Tom Guu wrote: > Dear Dr. Meng, > > This is Tom Guu from Rice University. I am using chimera to make > some animation for my virus structure, that I would like to present > at my defense ten days from today. I encountered a problem with > Chimera with the image storage issues. > > I am able to make movies, but they are generally very short, last > for a few seconds, and the frames are generally stored at a /tmp > folder. Since the /tmp folder in our computer server has quite > limited spaces, once I perform a more complex animation, errors > messages would pop up (each ppm is about 4MB and sometime that's > over 300 frames will fill up the tmp dictory). I am thinking about > storing frame files onto an external hard drive (200-300GB), which > can handle many more frames. So I go into 'movie recorder" under > which there is a "frame options". I specified the dictory for > frames to my external dirve (also clicked on "Set Input > Location"). Then re-execute my command (Open, click on cmd file > which cotains the script), well... the frames seemed to be stored > at the same /tmp location (nothing was written onto my external > drive). Is there a way that I can do to make the frames stored at > the external drive? If the frames are stored on the external > drive, is it going to affect the encoding process? > > In addition, I am also trying Chimera on my windows system > (Vista). I was able to excute the command (cmd files) without any > problem. The molecule is spinning as it should in the chimera. > However, when I opened up the encoded movie, it is just a blank > screen (with no molecule in sight). I check the directory (also > another /tmp directory), and I can see the ppm files were being > written. Then a screen popped up on my computer, C:\Program Files > \Chimera\bin\ffmpeg.exe The screen was on for at lesat 20-30 secs, > then the movie is made. However, as I said, I didn't see any movie > on my computer screen though I did find the "help command" and I > am currently don't seem to be able to find the answers to my > problems. Any suggestion? > > Thanks for such a long email. I much appreciate your help. > > Regards, > Tom Hi Tom, If you are using the movie command to record the movie, you should use the movie command options to specify the directory (for example, a command something like "movie record directory my-directory-path"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> The "frame options" in the Movie Recorder graphical interface only affect recording with that graphical interface, not with the command. However, if you *are* using the Movie Recorder to record and it seems to be ignoring your setting, please use "Help... Report a Bug" in the Chimera menu to send us a problem report. Include a description, and if you want feedback, your email address. I am not sure I understand your second issue. All I can say is that even though a movie file may appear, it takes a while for the ffmpeg program to fully create it, so you have to be patient and wait until ffmpeg is done before you can open the movie and play it back. Was the movie OK after ffmpeg was done? If not, again you may want to use "Help... Report a Bug" and include any relevant information. This mechanism also allows files to be attached to the report. Besides "help command" for commands (for example, "help movie" to see your local copy of the URL given above), the Chimera Help menu provides several routes into the documentation (including "Help... Search documentation") and you can click the Help button on most dialogs to see the corresponding manual pages. For future reference, it is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu than to me personally, unless you are including private data. This allows others to benefit from the information, and other staff to answer your question if I am unavailable or don't know the answer. Best wishes for success and triumph at your defense! Elaine ===== Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

displaying two surfaces
by Marcus Carr 14 Aug '09

14 Aug '09

I am trying to create a figure that encloses three residues in a protein in one surface and the rest of the protein in another. I put the three residues into one group using surfcat and the rest of the protein in another. When I try adjust the surface transparency, the three-residue surface all but disappears. If I set transparency to 0%, I appears normal. If I increase it even to just 1%, it almost completely disappears. It looks like wherever this three-residue surface is inside the protein surface, it only shows if the transparency of three-residue is set to 0%. All this is with the protein surface set to 50%. I'm not sure whether this list accepts attachments, but I put in screen shots of what it looks like. marcus

3 2

Scripting with Chimera
by Lockwood, Svetlana 13 Aug '09

13 Aug '09

Hi All, Here's my problem: I need to calculate hydrogen bonds for several thousand PDB files. Chimera has nice hbonds command line command - sweet! Since Chimera was vanishing from Ubuntu, I had to switch to other available tools, i.e. Windows. After I got my python up and running and communicating with Chimera modules. Here's my very simple pseudo-idea: foreach file in the list: open PDB file construct output filename from input filename calculate & and write out hydrogen bonds using hbonds command close file end foreach Short and sweet. Except that one cannot use a command line command within python code. Command files don't work either because they do not understand python commands. Someone must have run into the same problem before me :-) Is there a way around this problem? Thank you, Svetlana

2 2

Dr. Simon Sauve is out of the office.
by Simon Sauve 13 Aug '09

13 Aug '09

I will be out of the office starting 2009-08-07 and will not return until 2009-08-24. You can reach me at simsauve(a)yahoo.ca & 819-776-2134 (cell: 819-923-2143). In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155

1 0

Saving session with IMOD model
by Bui Khanh Huy 13 Aug '09

13 Aug '09

Hi all, I opened an IMOD model in Chimera. After I opened a saved session with Chimera, the IMOD model disappeared. Is this because of my version (alpha 1.4 (build 26844))? Best, Huy -------------------------------- Huy K. Bui Institute of Molecular Biology and Biophysics Swiss Federal Institute of Technology (ETH Zürich) ETH Hönggerberg, HPK F7 CH-8093 Zürich, Switzerland phone: +41 1-633-2462 fax: : +41 1-633-1073 e-mail: huy.bui(a)mol.biol.ethz.ch <mailto:huy.bui@mol.biol.ethz.ch>

3 2

command 'buriedArea'
by Harinathachari Bahudhanapati 12 Aug '09

12 Aug '09

Hi all, Could you explain the command 'measure buriedArea' ? I am trying yesterday's daily build. Could you give me an example how to use this command? I think I am mangling the command, somehow. Could you help me? Thank you very much. Sincerely, Hari

3 3

Orientation and quaternion
by Damien Larivière 06 Aug '09

06 Aug '09

Dear all, In the attached image, two copies of the FtsZ protein (pdb 1FSZ) are displayed in Chimera. I would like to know the orientation of one copy with respect to the other one. Is there a way to get this information ? Is it possible to get a quaternion instead of a set of Euler angles ? My best regards Damien

2 1

Q about opening two structures in the same window
by Farhana F Syed 06 Aug '09

06 Aug '09

Hello, I recently downloaded chimera and have been using to view my protein homology model - mainly to show the 2 residues that could be involved in binding to a molecule inside the cell. For that purpose, I need to be able to open the small molecule (citrate or phosphate) in the same window with protein; so I can show the small molecule binds to the specific amino acid residues. But even if I open the two together, how do I pick the small molecule and move it around where I need it? Please help. Thanks, Farhana

2 1