November 2007 - Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] ppt and movies
by Elaine Meng 22 Nov '07

22 Nov '07

Hi Markus, I can answer this one: > Why does the command movie record supersample 3 give virtually the > same file size then just movie record? Supersampling in Chimera initially saves a larger image for each frame but then samples it down to the requested size. This reduces "stairstepping" along edges without changing the pixel dimensions of the image that is ultimately saved for each frame. It increases calculation time rather than file size. Supersampling is also an option for saving individual images (File... Save Image) when you are not raytracing. You can see the difference provided by this feature independent of the movie-encoding process by comparing images saved with and without (1x1) supersampling. 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] chimera help - surface exposed sides
by Elaine Meng 22 Nov '07

22 Nov '07

On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote: > Hi Elaine, > I am trying to find an easy way to determine solvent > accessible/surface exposed side chains but also buried side chains > from atomic structures. > The idea would be to: > - display the surface > - have a command that would highlight (color) surface exposed side > chains/amino acids > Optional: color the identified aa by physical property, etc > - show all the identified amino acids on a primary sequence > - write out the amino acids into a text file. > > Would be great if you can let me know, how to do this most efficiently. > Thanks, > -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) > Hi Thomas, - First assign atoms (or residues) an attribute with values equal to their solvent-accessible surface areas (more details below). - Then you can use Select... By Attribute Value to select any subset of those based on some cutoff, for example all atoms with surface area > 0. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#select The selection can be written as a list of atoms (or residues) with Actions... Write List, and the Sequence tool will show the current selection on the protein sequence (it would also be shown on a multiple sequence alignment associated with the structure, if you have such an alignment). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html - Of course you could also color the selection, but now that numerical attributes are assigned, you can map values to colors that will gradually shade from one to another with "Render by Attribute" or the command "rangecolor" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html Now, back to how to get the attribute values assigned. Currently it is necessary to use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis). It sends coordinates to the NIH StrucTools server. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html We are in the process of generating our own surface-calculation code that will provide these values within Chimera, but it is not done yet. The main inconvenience of this server approach is that you should first delete things like water and ligands if you don't want them lumped with the protein during the calculation. "Area/Volume from Web" has a few different options of what is calculated. You can use its MSMS method to calculate both molecular surface and solvent-accessible surface (this will generate two attributes) or the Gerstein method to calculate solvent-accessible surface. Atom attribute values will automatically be assigned by this tool. If you want them summed to residue attribute values, you must also use "Attribute Calculator". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html There are examples of using Area/Volume from Web, Attribute Calculator, and Render by Attribute in the Attributes tutorial, part 2: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html#part2 I hope this helps, 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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Coloring a surface according to distance from a selection
by Paul.Pillot＠ac-nice.fr 21 Nov '07

21 Nov '07

Hello, I can color a surface according to the distance from a single point or a plane, but is it possible to do it according to the distance from a selection (eg an other chain or molecule) ? My aim is to show the contacts between an antibody and an antigen. I tried the tool intersurf for doing it, but the result is pretty crude (low definition of the surface compared to the usual surfaces available). Thanks in advance, Paul

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spaceball 5000
by Jean-Paul Armache 20 Nov '07

20 Nov '07

hello, i have a question regarding usage of a 3d manipulation device. i have a spaceball 5000 device, which i would like to use under linux (or windows). is there a way of using this device in chimera? best regards, Jean-Paul Armache AG Beckmann LMU Gene Center

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