- Chimera-users - RBVI Mailing Lists

scripts in Chimera
by Ben Keshet 29 Oct '08

29 Oct '08

Hi, I am reviewing a large number of structures (docking results). I uses the ViewDock tool which is great and makes life much easier. Still, for every file I open with ViewDock, I repeat the same set of commands before actually reviewing the poses, that is (initially only the receptor structure is open, with only ribbon shown): 1. open the ligands mol2 file. 2. color by element 3. choose atoms within 6A from the ligands (by selecting the ligand, than select zone<6A). 4. show the selected atoms. This is to show only receptor atoms within 6A of the ligand. Is there a way I can "record" this sequence or write some simple script that I could run after opening the ligands mol2 file? Thanks! Ben

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volume planes display loop
by Benoit Zuber 28 Oct '08

28 Oct '08

Hi, I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299? Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value. Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)? Finally, can all of this be specified through the command line? Cheers, Ben Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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Flushing output during the script execution
by Lukas Palatinus 27 Oct '08

27 Oct '08

Hello all, I am using Chimera as a visualization tool for small-molecule electron densities obtained by ab initio structure solution. I want to create a small script that will make Chimera read and display the intermediate electron densities as they are produced during the iterative structure solution process. I am not skilled in Python, but I could make a simple Python script by copying and modifying scripts previously posted in this list. Here is the script: from chimera import runCommand as run from os.path import exists from time import sleep map_file= 'test.xplor' while exists(map_file): run('close all') run('open ' + map_file) sleep(1) I am sure this is not the most elegant way to achieve what I need, but it should do the job. What the script should in my opinion do is to read and display the file test.xplor, then wait one second, close the map and reopen it again, until the file test.xplor is deleted. The script does >>almost<< that, it opens the volume viewer, reads the map, but it does not display the map in the main Chimera window. Only after the file test.xplor is deleted, the last map is displayed. Can anybody give me a hint what am I doing wrong? I am using Chimera 1.2540 on Mac OS X 10.4. Thanks in advance for any help. Best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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forget previous error
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Sorry, I made a mistake and found my problem. All the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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: Divendres, Octubre 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 66, Issue 22 > 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. volume planes display loop (Benoit Zuber) > 2. Re: volume planes display loop (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 24 Oct 2008 16:36:42 +0100 > From: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Subject: [Chimera-users] volume planes display loop > To: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4901EB8A.9040102(a)mrc-lmb.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I have got some questions regarding plane display of volumes: > Is there a way to cycle through a limited range of planes? For > example > if the thickness of my volume is 300, is it possible to cycle from > z = > 100 to z = 120, instead of from z = 0 to z = 299? > > Is there a way to make the cycling through the planes start in the > other > direction than when it stopped last time? For example, I click stop > while the display is cycling from low z value to high z value. If I > then > click start, the display is going to cycle again from low to high z > value but I would like it to cycle from high to low z value. > > Is it possible to specify a starting plane and an end plane, and to > have > the display going from the starting plane to the end plane only > once > (without cycling)? > > Finally, can all of this be specified through the command line? > > Cheers, > Ben > > > Beno?t Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber(a)mrc-lmb.cam.ac.uk > > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Oct 2008 10:31:44 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] volume planes display loop > To: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Cc: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <49020680.2070802(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ben, > > The current Chimera daily builds have a more flexible volume > plane > cycling interface. In the planes panel it now has a switch > > Cycle through [20] planes at speed [30] > > It lets you play through a specified number of planes centered on > the > currently shown plane. You start it by clicking a switch and stop > it > the same way. There is no control to stop after N planes, and the > initial direction of play is the same as when you last stopped > playback. > There is currently no Chimera command equivalent which would > obviously > be handy for making movies. I've attached a Python script which > can be > used with Chimera commands (example given in script) to control > exactly > which frames to show in a movie. Note that the frame rate is only > relevant for real-time cycling in Chimera. Movie recording > captures > every new frame no matter how slow they are rendered and plays in a > movie player at 25 frames per second (adjustable with a movie > encode > command option). Chimera movie recording capabilities are very > limited > now but it is an area we intend to improve. > > Tom > > > Benoit Zuber wrote: > > Hi, > > > > I have got some questions regarding plane display of volumes: > > Is there a way to cycle through a limited range of planes? For > example > > if the thickness of my volume is 300, is it possible to cycle > from z = > > 100 to z = 120, instead of from z = 0 to z = 299? > > > > Is there a way to make the cycling through the planes start in > the other > > direction than when it stopped last time? For example, I click > stop > > while the display is cycling from low z value to high z value. If > I then > > click start, the display is going to cycle again from low to high > z > > value but I would like it to cycle from high to low z value. > > > > Is it possible to specify a starting plane and an end plane, and > to have > > the display going from the starting plane to the end plane only > once > > (without cycling)? > > > > Finally, can all of this be specified through the command line? > > > > Cheers, > > Ben > > > > > > Beno?t Zuber > > MRC Laboratory of Molecular Biology > > Hills Road > > Cambridge > > CB2 0QH > > United Kingdom > > +44 1223 402209 > > bzuber(a)mrc-lmb.cam.ac.uk > > > > _______________________________________________ > > 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 > > > End of Chimera-users Digest, Vol 66, Issue 22 > ********************************************* >

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Problem with sum?
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Hi guys, I got back to the script on inertia axis calculation and I had the following error when running it on the built of th 15/10/2008 on my linux box: Traceback (most recent call last): File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 73, in <module> axes, d2, center = inertia_ellipsoid(m) File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 13, in inertia_ellipsoid mass = sum(amass) TypeError: 'float' object is not callable then I just try in the python shell: i=[1,2,3] sum(i) and I have the same prob. sum(i) Traceback (most recent call last): File "<pyshell#38>", line 1, in <module> sum(i) TypeError: 'float' object is not callable Some input? all the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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, Març 19, 2008 8:43 pm Assumpte: Chimera-users Digest, Vol 59, Issue 19 > 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. Re: Principal axis of inertia (Tom Goddard) > 2. problem with 17/03 build linux 64 (Jean-Didier Mar?chal) > 3. Un-tile (Jim Nettles) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 19 Mar 2008 12:00:33 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Principal axis of inertia > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47E162D1.5070108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Eric, > > Just ignorance -- didn't know Chimera could tell me the atomic > mass. > Attached is the same script only using atomic mass instead of > atomic number. > > Tom > > Eric Pettersen wrote: > > Just wondering why you weighted by atomic number rather than mass > > > (a.element.mass)? > > > > --Eric > > > >

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Re: [Chimera-users] coloring seperate domains
by Elaine Meng 23 Oct '08

23 Oct '08

On Oct 22, 2008, at 1:52 PM, Chin-Hsien (Emily) Tai wrote: > > We would like to use Chimera as a visualizing/figure drawing tool to > compare different domain parsing schemes and we are wondering how to > automate the process as much as possible. The tasks are: > 1.fetch a PDB > 2.select Chain (for example B) > 3.Invert (all models) > 4.Atoms/Bonds delete > 5.chain trace only > 6.backbone only > 7.Ribbon show rounded > > I am wondering if there is a simple way to combine step 1 to 4 to > display only specified chain in PDB? > Then rotate the structure to minimize domain overlapped area. > > Then color each domain according to different parsing schemes, for > example: > scheme1 "color red #0:1-38.A 150-190.A; color green #0:39-149.A; > color blue #0:192-347" > scheme2 "color red #0:1-30.A 160-195.A; color green #0:31-159.A; > color blue #0:196-347" > > Can Chimera read a script and displays different domains in > different colors? > Thanks for your advice in advance! > Cheers, > Emily, Dear Emily, You can definitely do all those steps in a script, except I'm not sure how to automatically orient the structure to best show the domains. I'll discuss the other parts first. A Chimera command script is just a text file containing the same things you would enter at the command line. If you name the file something.com or something.cmd it will automatically execute when opened in Chimera (with File... Open or the command "open"). Chimera can also execute python scripts (something.py) in the same way. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > There are many possibilities for either type of script, but here are some example Chimera commands: open 2mnr delete ~ :.a ribbon ribrep rounded ~disp color red :3-132 color dodger blue :133-359 copy png file 2mnr.png This set of commands fetches PDB structure 2mnr, deletes everything that is NOT chain A, displays ribbon, uses the rounded ribbon style, undisplays all atoms, colors the specified residue ranges, and saves an image in PNG format. You don't have to specify the chain in the coloring command since there is only one chain left. Each of these commands has a manual page if you want to see details (for example, there are other image formats such as TIFF). You can try the commands in the Command Line to see what works before putting them into a script. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> For saving images, you might want to make the background white (set bg_color white) before using the script, or after opening each structure use the ribbons preset and then a publication preset (preset apply int 1; preset apply pub 1) instead of ribbon and ribrep rounded. <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/print.html#tips> There are some fancier approaches that may facilitate processing a large number of structures. You can separate the structure-specific and general commands using aliases: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png # # the following general commands could be put in a separate file # open mypdb delete ~ mychain preset apply int 1 preset apply pub 1 color red dom1 color dodger blue dom2 color yellow dom3 color magenta dom4 copy png file output close 0 This structure only has two domains, so I clear any previous dom3 and dom4 assignments from previous structures. There will be error messages when commands refer to nonexistent aliases, but they can be ignored. The reason you might want to separate the specific and general commands is that all of the general commands can then be put in a second command file (for example named "process.com" ) that is opened by the first script. The second script file could be in the same directory (folder) as the first, or you could specify its whole pathname. alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png open /Users/meng/Desktop/process.com # # now go to next structure # alias mypdb 4enl alias mychain :.a alias dom1 :1-141 alias dom2 :142-436 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/4enl.png open /Users/meng/Desktop/process.com [... etc.] Putting the general commands in a separate file minimizes the number of lines in the primary command file. However, it may still be tedious if you are processing a very large number of structures. Since I don't know python, I would probably write a script or program (in some other language) to make the long main Chimera command file. If you know python, another approach is to make the main script python instead of Chimera commands, and have it cycle through multiple structures. You could call the Chimera commands in my examples from inside the python script. Finally, now about orienting the structure to best show the domains. The only way I can think of with Chimera commands is to use "align" to put domains 1 and 2 front and back, then rotate 90 degrees, for example: align dom1 dom2 turn y 90 That worked pretty well in my tests. Those commands could be in the general script (process.com in my example), assuming all the structures have at least two domains, before the image-saving command. There are some other possibilities that require python; I'll get back to you if we come up with something good. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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Re: [Chimera-users] Chimera-users Digest, Vol 66, Issue 20
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Hi All, I figured it out. The problem turned to be the resolution of the files that did not play in the powerpoint. Editing the movie to have a lower resolution enabled the file to play fine in the powerpoint. I wonder if there can be an option to determine the resolution in the output file from Chimera to avoid such problems with powerpoint and also, this can be added to the tips on Chimera site for making the movie for use in powerpoint: "make sure of the produced file to match the projector and the computer. Usually, something like 800x600 should work" Thanks to Elaine for her help. Ibrahim On 10/22/08 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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. Question about movie in powerpoint (Ibrahim Moustafa) > 2. Re: Question about movie in powerpoint (Elaine Meng) > 3. Re: orthogonal views (Elaine Meng) > 4. Re: orthogonal views (Tom Goddard) > 5. Re: orthogonal views (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Oct 2008 13:05:51 -0400 > From: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Subject: [Chimera-users] Question about movie in powerpoint > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C524D5AF.343C%I.moustafa(a)psu.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera team who is always giving the best support, > > I have a question regarding movie playing in power point and hope you can > help. > > I'm setting a power point presentation and want to play some movie (.avi > MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; > however, if I'm in the presenter view mode it does not play and gives me a > black screen. > I tried to re-insert the movie, change the view size, put everything in the > same place...but none of these solved the problem. > > The funny thing is that other movies bigger in size can play fine in the > presenter view mode. These have the same format (avi MSMPEG-4v2) and created > using the same program. > > Do you have any idea how to resolve this issue? Any advice is more than > welcome. > > Also, I noticed that sometimes the movie, that is known to be working > fine, does not work for unknown reason. > Especially in the case of 2 movies in the same slide. Any tips to have two > movies in the same slide to work in a more robust way is really appreciated. > > Really appreciating your help, thanks; > Ibrahim

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orthogonal views
by Thomas C. Marlovits 22 Oct '08

22 Oct '08

Hi Chimera's ... is there an easy way to create orthogonal views at the same time of a molecule ? The idea is to open a (pdb) file and visualize the molecule from orthogonal directions at the same time in one viewer. Rotation/ movemements of the molecule should be done then on all three views at the same time of course. Maybe you have already implemented such an option (similar to the stereo viewing ...) Tx, -T. ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader 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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Question about movie in powerpoint
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Dear Chimera team who is always giving the best support, I have a question regarding movie playing in power point and hope you can help. I'm setting a power point presentation and want to play some movie (.avi MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; however, if I'm in the presenter view mode it does not play and gives me a black screen. I tried to re-insert the movie, change the view size, put everything in the same place...but none of these solved the problem. The funny thing is that other movies bigger in size can play fine in the presenter view mode. These have the same format (avi MSMPEG-4v2) and created using the same program. Do you have any idea how to resolve this issue? Any advice is more than welcome. Also, I noticed that sometimes the movie, that is known to be working fine, does not work for unknown reason. Especially in the case of 2 movies in the same slide. Any tips to have two movies in the same slide to work in a more robust way is really appreciated. Really appreciating your help, thanks; Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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About Amber residue number renumbering
by Francesco Pietra 22 Oct '08

22 Oct '08

Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra

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