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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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Re: [Chimera-users] [Fwd: Re: Chimera hide all models button]
by Eric Pettersen 27 Nov '07

27 Nov '07

I guess I do have some tips to offer here. You can use the "Configure..." button of the Model Panel to change what happens when you double click on a model. By default, double clicking shows the attributes of a model. You can have double click do any combination of button actions, so you could instead have double click both "show only" the model and "activate only" the model. With that configuration, if you wanted to show and activate two specific models you would click on one model and then control-double- click on the other one. If you want to show and activate all models you would click on the first model listed in the Model Panel and then shift-double-click the last model. --Eric On Nov 27, 2007, at 8:57 AM, Tom Goddard wrote: > Eduardo thinks we need better controls for showing just one or two > models and activating just one model when many are present. > > -------- Original Message -------- > Subject: Re: Chimera hide all models button > Date: Tue, 27 Nov 2007 08:34:07 -0700 > From: Eduardo Sanz-Garcia > To: Tom Goddard > > > Tom Goddard wrote: >> Hi Eduardo, >> >> Perhaps clicking on the "Shown" heading in the Model Panel could >> hide all models if all are shown, or show all if all are hidden. >> If some are hidden and some are shown maybe it would show all, >> then a second click would permit you to hide all. I don't really >> like this idea because very few people would know to try it. >> Usually clicking on list headings sorts using that column. > That is true. I didn't realize about this. >> Although sorting may seem not too useful for the "Shown" column I >> can imagine if you have 50 models open with just a few shown you >> might want to sort to bring those to the top. >> >> A slightly harder way to show just one model is to select its >> line in the Model Panel and press the "Show only" button in the >> right column of buttons. Unfortunately that button is way down on >> that scrolled list of buttons. You can hide many of those buttons >> using the "Configure..." button on the Model Panel and it will >> remember the hidden ones in your preferences file. But there is >> no way to reorder the buttons as far as I know. >> >> The oval next to the step size above volume histograms allows you >> to show/hide that map. Maybe I could enhance that so if you use >> the right mouse button instead of the left then it shows that map >> and hides all others. Cryptic but not unexpected behavior. > Yes, this is a little cryptic but a fast method. >> Still there are only 3 histograms shown by default. Perhaps if I >> added the scrollbar for the histograms as you suggest that would >> further improve switching display between individual maps. > I believe that the scrollbar is a very good idea! > > I believe that Chimera should improve the way to show or activate > all the models faster from the GUI. I spend a lot of time > activating two models, deactivating the rest, and showing only > these two models. The command line is fast but there are some, like > me, that always forget the commands. >> >> Let me know what ideas you think are best. It is quite difficult >> to make the user interface simple to use and powerful. Thanks for >> your ideas. >> >> Tom >> >> Eduardo Sanz Garcia wrote: >>> Do you mind if I share a very personal suggestion? >>> I always open 5 or more maps at the same time (chimera >>> directories*/*100.map) . I normally want to examine each >>> individually, and then compare them. I would like to undisplay >>> all of them at the same time. I know that this is possible from >>> the command line (~modeldisplay), but I always forget it. It >>> would be nice to have the same function from the GUI. I am >>> suggestion to be able to click in the black circle (bottom image) >>> and un/display all the models at once. >>> >>> Anyway, thanks for the volume viewer capabilities of chimera. >> >> >

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How do I
by Eduardo Sanz Garcia 27 Nov '07

27 Nov '07

I am using Chimera alpha version 1 build 2467 2007/10/31 I liked how each volume map opened has a different color. That's a great idea!! But I have a problem, I am displaying 4 volume maps at the same time. The volume viewer window only shows 3 histograms, therefore to modify the threshold of the fourth I have to close one of the volumes. Is there a way to modify the fourth histogram in the volume viewer window without close another? I also found a different behavior if you close the upper, middle and bottom histogram. Thanks.

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saving color palette
by William Jeffrey Triffo 26 Nov '07

26 Nov '07

is there a way I can save the color palette to a file? I realize it seems to be saved as a user setting somewhere because it always pops up again in the same configuration as the previous session, but I would like to be able to back it up intentionally if possible. Also, is it possible to save/load various palettes? thanks, -Jeff --

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Chimera vs Amber, which one digresses from the average pdb rules?
by Francesco Pietra 26 Nov '07

26 Nov '07

A lipid/water pdb file that was good for Leap (Amber9) to get top/crd, once passed through Chimera 2470 to remove residues is no more good for Leap. All TER were removed by Chimera, ATOM renamed HETATM, while CONECT records were added. As such, Leap said: In file [chirality.c], line 142 Atom named C217 from POP did not match Aborting I knew such type of message. There is no C217 atom. On previous (different) occasions, insertion of TER records put the house in order. I inserted all TERs between POPC residues and between WAT residues (thanks to Python!). Now Leap said: In file [atom.c], line 444 bond AtomProblem found Aborting As I did not know this type of message, I tried to investigate that line 444. Following vim's command :n,444 that line, indicated at bottom of terminal as "444,1", reads HETATM 441 O31 POPC 5 -44.082 -12.831 14.685 1.00 0.00 O A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads HETATM 444 C32 POPC 5 -46.343 -12.925 15.140 1.00 0.00 C In the original (good for Leap) pdb those lines read: ATOM 441 O31 POPC 4 -37.722 -19.453 18.019 1.00 0.00 L11 O ATOM 444 C32 POPC 4 -39.844 -19.273 18.941 1.00 0.00 L11 C Chimera also changed atom names, such as in the final part of the POPC residue (Sybyl naming?, if so, there is an alternative in Chimera not to follow Sybyl rules?) HETATM 528 XH14 POPC 5 -47.646 -9.424 -0.112 1.00 0.00 H HETATM 529 YH14 POPC 5 -46.217 -10.553 -0.172 1.00 0.00 H HETATM 530 5C31 POPC 5 -47.890 -11.168 -1.419 1.00 0.00 C HETATM 531 XH15 POPC 5 -47.763 -12.309 -1.296 1.00 0.00 H HETATM 532 YH15 POPC 5 -48.986 -11.063 -1.417 1.00 0.00 H HETATM 533 6C31 POPC 5 -47.242 -10.566 -2.756 1.00 0.00 C HETATM 534 XH16 POPC 5 -46.135 -10.759 -2.831 1.00 0.00 H HETATM 535 YH16 POPC 5 -47.802 -11.112 -3.597 1.00 0.00 H HETATM 536 ZH16 POPC 5 -47.451 -9.454 -2.737 1.00 0.00 H TER which, in the original (good) pdb was: ATOM 528 H14X POPC 4 -38.665 -14.879 4.398 1.00 0.00 L11 H ATOM 529 H14Y POPC 4 -39.080 -16.603 3.952 1.00 0.00 L11 H ATOM 530 C315 POPC 4 -40.370 -15.221 2.996 1.00 0.00 L11 C ATOM 531 H15X POPC 4 -41.330 -15.752 3.099 1.00 0.00 L11 H ATOM 532 H15Y POPC 4 -40.694 -14.148 3.019 1.00 0.00 L11 H ATOM 533 C316 POPC 4 -39.787 -15.573 1.664 1.00 0.00 L11 C ATOM 534 H16X POPC 4 -39.553 -16.661 1.544 1.00 0.00 L11 H ATOM 535 H16Y POPC 4 -40.534 -15.211 0.948 1.00 0.00 L11 H ATOM 536 H16Z POPC 4 -38.782 -15.094 1.533 1.00 0.00 L11 H TER Although it is not clear to me yet where really Leap crashed (nor am I placing Leap as the standard; simply I have to get top/crd from it, if I want to carry out MD with Amber). Elaine already kindly clarified the ATOM/HETATM issue. I hope now to get help about the atom names , ie a table of conversion to get Leap working or a not-Sybyl choice in Chimera. Once again, I regret very much to pose so many problems of language. Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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<< Rendering proteins with Chimera >>
by Hatuey Hack 23 Nov '07

23 Nov '07

Hi all, As a Chimera new users, I notice that the proteins are rendering different depending on the program they where prepared. I used the preset to render them. I have a protein with all residues in different color and the other protein is rendered in a single color. My question is: this is a problem of Chimera or it is a problem with the protein file? Regards, Hatuey

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Aligning a protein into a membrane
by Francesco Pietra 22 Nov '07

22 Nov '07

Elaine: Relating to your instructions of last 19 Nov (I printed your mail, then unfortunately I deleted it) how to align a protein into a membrane (for both I have valid pdb and valid Amber parameters) I am probably made elusive mistakes at the stage of saving new pdbs. I aligned the protein into the membrane, then (with protein selected and membrane not active) I saved the new pdb, getting two files, "0" for the membrane and "1" for the protein. In Amber LEaP both these pdb file could be loaded and combined, however save top/crd failed because something was wrong with the membrane file. In fact, if the original pdb for the membrane is used, top/crd can be saved, though the protein is not accurately aligned. Clearly, my plan is to remove superimpositions among molecules for the "whole" obtained from Amber. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

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