July 2008 - Chimera-users - RBVI Mailing Lists

How to print molecular structures?
by �� 28 Jul '08

28 Jul '08

Hi all, I want to print 1000 molecular structures one by one. I am wondering if it is possible to print molecular structures by Chimera. If it is not, are there some other software can do this? Please kindly advice. Any answer would be appreciated! Best regards, Yolanda Guo Northeast Normal University

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Pointers to writing extensions in chimera
by Mario J. Borgnia 25 Jul '08

25 Jul '08

Hi all, I would like to try and write an extension to chimera. Could anyone give me some pointers on where to find the tools necessary to do so. Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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BIOMT matrix in Chimera?
by Francesco Pietra 25 Jul '08

25 Jul '08

>From a homotrimer pdb template I have created (with Modeler) a homology model, with very good score, using a single subunit. Is it possible with Chimera to create the homology homotrimer, as this is what I need? To this concern, the original pdb for the template includes the BIOMT transformation matrix for both crystallographic and non-crystallographic operation. That is, the pdb includes as many identical chains to open directly the homotrimer for the crystallographic pose. Is that BIOMT matrix usable by Chimera for the homology model? Or the way ti take is another one? I used much technical language, well above - however - my expertise in these affairs. That in view of any help, for which I'll be most grateful. Thanks francesco pietra

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nogui vrml export?
by Paul 25 Jul '08

25 Jul '08

Hello, Is there any way to export .vrml or .wrl in the nogui mode? The idea would be to run a script that would load a .pdb file and transform it into a few different representations and then export them. I saw in previous posts that there is no support for exporting images in this mode. Thanks, Paul

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superimposing active sites
by Elaine Meng 24 Jul '08

24 Jul '08

On Jul 23, 2008, at 6:18 PM, Maria wrote: > Elaine, > I have created active sites by using the zone in > chimera for 72 proteins. Is there a way I can > do structural superimposition of the active > sites using chimera? > Thanks, > Maria Hi Maria, Sure, there are many, many ways to superimpose structures in Chimera. If the structures are homologous (have the same fold, usually also some sequence similarity), probably the easiest are these two methods: (A) MatchMaker tool (or the "matchmaker" command, which acts exactly the same way) - it creates a sequence alignment and then uses those alignment columns to superimpose the structures (B) if you already have a sequence alignment, you can open that in Chimera and use it to superimpose the structures With both (A) and (B) you would use the whole structures - it is OK if you are only displaying a zone as long as the other atoms are still there (are merely hidden, not deleted). Some other approaches can be used for either homologous or nonhomologous proteins: (C) "match" command - you specifically name the atoms you want to use for fitting in the command; for example, atoms from a few active site residues and/or from the ligand (D) interactive fitting "by hand" Links to more detailed information... Discussion and examples of more than one method: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#s… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#com… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match… MatchMaker man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… "matchmaker" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html "match" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Using a pre-existing sequence alignment: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/fr… (see "Structural Superposition" section) Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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making MD movie
by bala 24 Jul '08

24 Jul '08

Hello freinds, While recording a MD movie or saving an image, chimera considers full screen ares. Is there any way that i can select a particular area in the screen and ouput the image or the MD movie accordingly. Thanks, Bala

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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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Chimera-users July 2008