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Movie recording does not stop
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Jean-Paul, The script you sent works for me with Mac X11 Chimera 1.2540 on Mac OS 10.4.11. I open two maps and the resulting movie is correct. You don't have any motion going on like a "roll" do you? Because the first line of this script "wait" with no frame count means that subsequent lines of the script will not be executed until all motion ceases. Likewise you have wait command with no frame count on the first two transparency setting lines. Tom Jean-Paul Armache wrote: > Thank you for the reply. It seems that I have today a lot of questions. > There is one more: > I have a script. When not in movie recording mode, it works fine. > However, if I input movie record and at the end movie stop and encode, > then at some point the script stops. Once it stopped with the labels, > so at the end I removed the labels. Now I have one map visible and I want > it to slowly get transparent to a point when it is no longer visible. > And here lies the problem. The script is fairly easy: > > wait; > movie record directory /Users/jean-paularmache/tmp-chimera; > > volume #1 transparency 0.0; wait; > volume #0 transparency 0.0; wait; > > > volume #0 transparency 0.05; wait 3; > volume #0 transparency 0.1; wait 3; > volume #0 transparency 0.15; wait 3; > volume #0 transparency 0.2; wait 3; > volume #0 transparency 0.25; wait 3; > volume #0 transparency 0.3; wait 3; > volume #0 transparency 0.35; wait 3; > volume #0 transparency 0.4; wait 3; > volume #0 transparency 0.45; wait 3; > volume #0 transparency 0.5; wait 3; > volume #0 transparency 0.55; wait 3; > volume #0 transparency 0.6; wait 3; > volume #0 transparency 0.65; wait 3; > volume #0 transparency 0.7; wait 3; > volume #0 transparency 0.75; wait 3; > volume #0 transparency 0.8; wait 3; > volume #0 transparency 0.85; wait 3; > volume #0 transparency 0.9; wait 3; > volume #0 transparency 0.95; wait 3; > volume #0 transparency 1.0; wait 3; > > > #movie finished > movie stop; > movie encode bitrate 12000 mformat avi output > /Users/jean-paularmache/Desktop/firstmovie.avi > > > > Ok, what happens is that Chimera generates endless amount of images. > Really, without cease. Now, if I do "movie stop;" from the command > line, it generates the avi file. However, the whole avi file consists > of one frame movie (meaning that even though it has the right amount of > frames, all are just one frame). > What is more surprising is that with other scripts this transparency > works. It is just right here that it doesn't want to cooperate. Could you > think of any reasons it might be behaving like that? > > > Best regards, > > Jean-Paul Armache

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StrucMeasure and distance
by Jean Didier Pie Marechal 23 Jul '08

23 Jul '08

Dear all, a small question. I know how to calculate the distance between two atoms calling the "distance" command and I generally use it embedded in the scripts I write. However, this time, I'd like to have access through my script only to the values of the distances (nothing related to the display) in order to stock them. I thought I would find my way through by using the StructMeasure module, but I am not able to do so. How could I just have a return of the distances between two atoms in the shell? Thanks a lot, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Agost 8, 2007 9:00 pm Assumpte: Chimera-users Digest, Vol 52, Issue 6 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. writing translation/rotation (Thomas C. Marlovits) > 2. Re: writing translation/rotation (Elaine Meng) > 3. Re: writing translation/rotation (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 8 Aug 2007 14:19:43 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.univie.ac.at> > Subject: [Chimera-users] writing translation/rotation > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <BAFCFCAA-D911-4E0C-8F5E-B41430E8E1B6(a)imp.univie.ac.at> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > am looking for an analysis tool in Chimera that would write out - > let's say a matrix for translation/rotation of a pdb-file in > respect > to another one. > > Usage: would like to align chain A and chain B present in a pdb- > file > and want to know which translation/rotation matrix has to be > applied > in order to convert the non-aligned pdb-coordinates of chain B to > the 'new" aligned pdb-coordinates. > > Thanx for your help, > -Thomas > > > > -------------------------------------------------------------------- > ---- > ------- > > Thomas C. Marlovits, PhD, M.A.S. > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > >

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Making a spin movie
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Andy, Here is a Chimera command script to make a movie that rotates the displayed models 360 degrees in 3 degree increments (120 frames) and writes the movie in Quicktime format (*.mov). movie record turn y 3 120 wait 120 movie stop movie encode output /tmp/movie.mov mformat mov bitrate 6000 Put this in a file with suffix *.cmd (e.g. spin.cmd) and open it with Chimera File / Open... or the open command to create the movie. Tom Anindito Sen wrote: > Hi Tom > Thanks for the reply. > > in the crystal structure- the region of interest (selected and > highlighted) lies in the interior. The idea is to make a movie of the > crystal structure rotating around the Y axis and one can visualize the > region of interest in a better manner. > > Therefore how can I generate a movie of this kind. > > Thanks > Andy

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Electron density map around selected residues
by Miles Pufall 23 Jul '08

23 Jul '08

Hello - I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera? Thanks - Miles Miles Pufall UC San Francisco

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vista chimera 1.2540 R6025-pure virtual function call error when opening pdb or mrc file
by Nils Woetzel 22 Jul '08

22 Jul '08

Hi, I have problems with chimera 1.2540 win32 and 1.2539 win32. it is working in version: 1.2524 win32 I installed it an windows vista business sp1. I have also installed visual studio 2008 (9.0). When I try to open either pdb or an mrc file I get the same error window: Title: Microsoft visual c++ runtime library text: Runtimje Error! Program: C:\Program Files\chimera\bin\pythonw.exe R6025-pure virtual function call. the debug command line option just brings: initializing graphics create application loading Tix loading Pmw creating main window creating menus creating toolbar creating lenses initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: 255 Press return or enter to to exit i try to open the pdb file (different files) before the return code: 255 I am not sure if the error actually comes from python.exe - but i could not find anything when searching for it. http://support.microsoft.com/kb/125749 explains the error, but i am not sure how to debug python code Is there a problem with that version of python or chimera with a visual studio installation or this runtime library error appearing independently of having visual studio installed or not. But the older release is working just fine: 1.2524 win32 so some new feature in chimera probably causes the error and might only show up in my environment?! Thanks Nils Woetzel Vanderbilt University

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surface rendering
by Peter Lewis 22 Jul '08

22 Jul '08

Dear Chimera-Users I've recently changed my computer to a quad core system which runs Red Hat and virtual Windows. I've installed chimera (32 bit) on both linux and windows. I have tried using chimera downloads posted in both June and July this year but cannot get surface rendering to work for either operating system. Is this a bug with recent versions of chimera, and if so, how do I fix it, or is it a bug with my new system? Any help gratefully appreciated. Peter A/Prof Peter Lewis Molecular Microbiology Group School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia Ph: +612 4921 5701 Fx: +612 4921 5472

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Movie contains overlapping windows
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Jean-Paul, Yes movie recording will include windows that overlap the Chimera graphics window. This is an unfortunate limitation of the Chimera image saving caused by it capturing images directly from the screen. On some platforms an overlapped window may not appear because the contents of the graphics window are saved even when another window overlaps. But that is not the case on most platforms. So in most cases the machine cannot be used for other purposes when a movie rendering is in progress. We have been interested in eliminating this limitation for some years but Greg Couch who handles image capture has not had time to get to it, If you use raytracing for the movie capture then it does not matter if the Chimera window is covered. But raytracing takes much longer to render. Tom Jean-Paul Armache wrote: > Hello again, > > I re-checked the spider loading, and now it seems to work. I don't > know why it did not previously. > > I have another question though. I have two versions of Chimera on my > computer now. I am using Chimera X Window to generate movies, > because in respect to the Aqua version, if I start another application > (like Keynote, web browser etc), the movie does not contain any parts of > the screen on top of it. > If I use the Aqua version (and on Linux is the same), it includes the > currently on-top graphics into the movie. Is there a way to not do so in > Aqua? > > Best regards, > > Jean-Paul Armache >

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10.5 mac Chimera hangs on resize
by Eric Pettersen 21 Jul '08

21 Jul '08

On Jul 21, 2008, at 4:32 PM, Jean-Paul Armache wrote: > Submitter Name: Jean-Paul Armache > Platform: (X11) Darwin 9.4.0 i386 > Chimera Version: production version 1 build 2540 2008/07/09 > Description > well, the X window tends to hang just after manually resizing the > window. Hi Jean-Paul, I was able to reproduce this and was able to come up with two solutions. One is to resize carefully. In particular, do not release the mouse button until you have stopped the mouse. I find that this always avoids the hang. The other solution is to upgrade your X11.app to the 2.3.0 version (as a prerequisite you need to be at OS X 10.5.4. or later). You can download 2.3.0 from here: http://xquartz.macosforge.org/trac/wiki/X112.3.0 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Problems saving eps files on Windows
by Julianne Chung 21 Jul '08

21 Jul '08

Hi, I am having trouble saving images in Chimera and was hoping that you may be able to help me out. I am running the latest version of Chimera on Windows. I have a molecule that I want to save as an eps file. I got to File --> Save Image --> Save As -->change the file type to eps and click Save, but no eps file appears in the directory I specified. Jpeg, png and tiff all work fine, but I can't get eps and ps to work. I've installed Ghostscript too, but that doesn't seem to help. Any suggestions are appreciated, Thanks, Julianne Chung Emory University

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Re: [Chimera-users] Possible image saving bug
by Walter Novak 21 Jul '08

21 Jul '08

Hi Elaine, I agree that some colors are shinier than others. Also, my brightness was not zero, but was the default of 1. I think however, I have tracked the issue down to the position of my lights. I had them pretty straight on and resetting this position gives the pov-ray shininess I was expecting. Thank you, Wally On Jul 17, 2008, at 9:29 PM, Elaine Meng wrote: > Hi Wally, > on to problem #2. > > I was unable to reproduce this problem. Are you sure that the > "brightness" is >0? If brightness is zero, there are no > highlights. Below are two images, the top with shininess 128 and > brightness 10, the bottom with shininess 128 and brightness 0. > Actually now that I look at it carefully, the bottom one confuses me > because the cyan things are still shiny, so I'm cc-ing the others > (Greg, any explanation??). The other colors in the bottom image are > non-shiny as expected, however! > > Best, > Elaine > > <imagebright10.png> > > > <imagebright0.png> > > > Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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