November 2007 - Chimera-users - RBVI Mailing Lists

distance measurement
by sette＠uniroma2.it 30 Nov '07

30 Nov '07

Dear all, I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do? Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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morphing structures
by Elaine Meng 30 Nov '07

30 Nov '07

> Thank you for your help. I did superimpose the structure with pdv > viewer. I did save as a pdb file but when I open the morph > conformations tool and I add the pdb I am not able to create the > interpolation between the structure. > > Do you know why? > Hi Djemel, I would recommend just using Chimera to superimpose the structures. Starting with the two structures in two separate files, open them with File... Open in the Chimera menu, then superimpose them. There are lots of ways to superimpose them but probably this simple command (show command line with Favorites... Command Line) will work fine: matchmaker #0 #1 In Morph Conformations you have to specify more than one structure. There should be more than one line in the Conformations list. My guess (and it's only a guess) is that the way the other program wrote the file it was considered all one structure, not 2 separate structures. 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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Detecting residue from command line
by Francesco Pietra 30 Nov '07

30 Nov '07

Sorry for a question that was surely answered many times. How to detect on the screen (from command line) residues from their resSeq number?. I have two different sets of WAT: 522-9999 and 0-4759 and want to check where 0-521 are located in a protein-ligand-POPC membrane. Thanks francesco pietra ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

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morphing movie
by Elaine Meng 30 Nov '07

30 Nov '07

> Actually I would like to do some movie with chimera but I never used > before. I have two crystal structure of two different conformation of > the protein that I work with. I would like to see the trajectory from > conformation 1 to 2. I just downloaded the chimera but I don't know > how to start. > > Could you tell me how to make the movie? I would appreciate you help. > Is that possible to load molecule 1 and 2 and see how the trajectory > is ? Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: November 30, 2007 10:29:41 AM PST It sounds like you want to use the Morph Conformations tool (under Tools... Structure Comparison). If you have two structures, it will "make up" a series of in-between structures to create a trajectory. You have to match (superimpose) the two structures yourself first. There are different options of how to make the in-between structures and how many to make. The trajectory-viewing tool, MD Movie, is automatically started to show the trajectory. From MD Movie you can record the trajectory as a movie file (Quicktime or other formats) or just save it as a PDB file for later viewing in Chimera. Probably you will need to learn a little bit about using Chimera so that you can set the display (ribbons, background color, displaying important sidechains) how you want for the movie. Chimera comes with a User's Guide. You can open it directly or search it from the Chimera Help menu. Also clicking the Help buttons on dialogs will automatically open the corresponding man pages. I will give some links to our Web site, but most of the same pages are included with your download. Tutorial on matching structures and making nice images: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Manual page for Morph Conformations: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (see the "Recording a Movie" section) For basic Chimera use, there is "Getting Started" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html and a more detailed version of that at our web site (not in the User's Guide): http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html but if you get stuck or have trouble finding something, you can ask me about it. 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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Re: [Chimera-users] Question regarding Chimera usage
by Tom Ferrin 30 Nov '07

30 Nov '07

------- Forwarded Message Date: Thu, 29 Nov 2007 20:06:54 -0800 From: swetha davuluri <swethadn(a)yahoo.com> To: tef(a)cgl.ucsf.edu Subject: Question regarding Chimera usage Dear Dr. Ferrin, I have a question Chimera usage. I am trying to fit a model to an EM map. I cou ld lock the map from moving but I am not able to transitionally shift the model . The translational shift box in "Fit Model in Map" is checked. Please let me k now how to transitionally move the model. Regards, Navya. _________________________________________________________________________ ___________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.ya hoo.com/ ------- End of Forwarded Message

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2D for 3D display
by Gang 'Gary' Ren 29 Nov '07

29 Nov '07

Hi, Chimera, I wonder how to create the 3D display by using the 2D image as below? http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png best regards Gary ---------------- Gang Ren, Ph.D. Phone: (415) 476-8284; Fax: (415) 514-2550 Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu Department of Biochemistry & Biophysics 1700, 4th Street, Byers Hall (QB3), room 301C San Francisco, CA 94143-2532

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Re: [Chimera-users] Chimera-users Digest, Vol 55, Issue 29 (heightmaps)
by Jonathan Hilmer 29 Nov '07

29 Nov '07

I would also be interested to learn how to do heightmaps in Chimera, or if it would be possible to add such a feature. Right now we use ImageJ (which doesn't have enough functionality) and Blender (which has too much), while Chimera would be perfect. In response to Gabe's question, it's not terribly convenient but you could use the Zone tool to generate just the 'positive' region and save that as a unique file. The 'combine.py' could then be used to subtract out the positive from the original, leaving the zeroed parent density file. Jonathan > Message: 1 > Date: Wed, 28 Nov 2007 22:12:40 -0800 > From: "Gang 'Gary' Ren" <gren(a)msg.ucsf.edu> > Subject: [Chimera-users] 2D for 3D display > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <web-5552878(a)msg.ucsf.edu> > Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" > > Hi, Chimera, > > I wonder how to create the 3D display by using the 2D > image as below? > > > http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png > > best regards > > Gary > > ---------------- > Gang Ren, Ph.D. > Phone: (415) 476-8284; Fax: (415) 514-2550 > Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu > > Department of Biochemistry & Biophysics > 1700, 4th Street, Byers Hall (QB3), room 301C > San Francisco, CA 94143-2532 > > > ------------------------------ > > Message: 2 > Date: Thu, 29 Nov 2007 10:23:49 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reverse "zone" tool? > To: Gabriel Lander <glander(a)scripps.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <474F03B5.5060609(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Gabriel Lander wrote: > > Hi Tom, > > is it possible to somehow make the "zone" tool in the volume viewer do > > the reverse of what it does? I have a PDB docked into a density file > > and I want to remove the density surrounding it so that it's easier to > > focus on the rest of the structure. > > By the way, I thoroughly enjoyed your demo of the new Chimera features > > here at the cryo course, I'm sorry I didn't have a chance to chat very > > much afterwards, > > Cheers, > > -gabe > > > > > Hi Gabe, > > One trick would be to use the "Color Zone" tool to color the surface > near the fit model completely transparent (hence invisible). Use menu > entry Actions / Color / From Editor, click the Opacity button and set > opacity to zero. Your molecule will be invisible. Then use Tools / > Volume Data / Color Zone, select all atoms (Select / Select All) and > press the color zone dialog Color button. Then go back and change the > color of the molecule to something visible. > > Three drawbacks of this approach. First, it doesn't allow you to > save the map with the region near the molecule zeroed out -- it is only > coloring the surface. Second, having a partially transparent surface > makes the rendering slower. Third, Chimera only handles one transparent > model correctly. If you try to add a second transparent surface you > will see odd effects, like the invisible patch blocks the second > transparent surface. If these limitations are severe, I can give you a > bit of Python code that actually makes a copy of the map with the part > near the molecule erased. > > Tom > > > ------------------------------

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Re: [Chimera-users] reverse "zone" tool?
by Thomas Goddard 29 Nov '07

29 Nov '07

Gabriel Lander wrote: > Hi Tom, > is it possible to somehow make the "zone" tool in the volume viewer do > the reverse of what it does? I have a PDB docked into a density file > and I want to remove the density surrounding it so that it's easier to > focus on the rest of the structure. > By the way, I thoroughly enjoyed your demo of the new Chimera features > here at the cryo course, I'm sorry I didn't have a chance to chat very > much afterwards, > Cheers, > -gabe > Hi Gabe, One trick would be to use the "Color Zone" tool to color the surface near the fit model completely transparent (hence invisible). Use menu entry Actions / Color / From Editor, click the Opacity button and set opacity to zero. Your molecule will be invisible. Then use Tools / Volume Data / Color Zone, select all atoms (Select / Select All) and press the color zone dialog Color button. Then go back and change the color of the molecule to something visible. Three drawbacks of this approach. First, it doesn't allow you to save the map with the region near the molecule zeroed out -- it is only coloring the surface. Second, having a partially transparent surface makes the rendering slower. Third, Chimera only handles one transparent model correctly. If you try to add a second transparent surface you will see odd effects, like the invisible patch blocks the second transparent surface. If these limitations are severe, I can give you a bit of Python code that actually makes a copy of the map with the part near the molecule erased. Tom

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Server and Client machines with different OS
by Isabelle Vergely 28 Nov '07

28 Nov '07

Hello, I know that it is possible to open one or several pdb files on a linux machine using a system command line like "> chimera [options] [input1 input2 ...]". My question is: Is it possible to use this command on a linux server to display chimera on a Windows client machine? Thank you very much in advance for your help. Best Regards. Isabelle

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ppt and movies
by Markus Voehler 27 Nov '07

27 Nov '07

I have recorded a movie of a pdb in chimera with the following command: movie record supersample 3 . . movie stop movie encode bitrate 6000 mformat avi output ./pol_b_movie.avi I can import it into ppt (2004, V 11.3.5) on my Mac (OS X 10.4.11) and it plays fine in the editing mode, but when I go to the slideshow and start the movie, there is a blank screen for the duration of the movie. When it is done, it shows the standing slide again. Any idea what might be going on? Also, is there a better way to improve the resolution then setting the bitrate to 6000, 30 f/s? I have tried the supersample 3 option, but this does not seem to make much of a difference in the final movie. Any input is appreciated. Markus

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