- Chimera-users - RBVI Mailing Lists

Ray Tracing Transparent Surfaces
by Damian Ekiert 22 Feb '11

22 Feb '11

Hello, Is it possible to raytrace a transparent surface in Chimera? I tried raytracing the frames of a movie where I fade in a surface, but the surface just appears abruptly, solid and black, then fades to the desired colors as the transparency approaches zero. Do I need to fiddle with the POVray settings or what? Any suggestions/work-arounds would be appreciated! Thanks, Damian Ekiert

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Selective surface colouring of aminoacids by hand
by Heinrich Lünsdorf 22 Feb '11

22 Feb '11

To whom it may concern. Dear colleagues, I am a novice in working with Chimera and a practicing electron microscopist. I learned to fit X-ray model data into EM-densities. My special question acutally is to select several surface exposed aminoacids by hand (either as a sequence ' aa #x to #y' or single aa '#5,67,577,579' etc.) as they have been epitope-mapped by antibodies and colorize them uniquely in the "MSMS main surface" mode of Chimera. How to colorize at the 'ribbon' I know already but I need this selective colorization at the 'Actions --> Surface --> Solid' level. How can I do this? Thank you coridally for your help in advance. Heinrich Lünsdorf ................................................................................................................................... [cid:image002.jpg@01CBD272.30DFF740] ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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animation suggestions
by Dougherty, Matthew T 18 Feb '11

18 Feb '11

1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script. 2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where & when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command. 3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing. 4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code. 5) I prefer to keep up with the daily builds & submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk. thanks for the good product. Matthew Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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animation suggestions
by Elaine Meng 18 Feb '11

18 Feb '11

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: February 18, 2011 12:12:35 PM PST > To: "Dougherty, Matthew T" <matthewd(a)bcm.edu> > Subject: Re: [Chimera-users] animation suggestions > > Well, there's always "stop" but it quits from Chimera, which may not be what you want. It does allow you to keep the entire contents of a script (you don't have to make a shorter version just to stop in that place). > Elaine > > On Feb 18, 2011, at 11:59 AM, Dougherty, Matthew T wrote: > >> Thanks Elaine & Tom, >> >> Is there a way to issue the escape key within a script? >> >> I thought of another suggestion: >> >> 6) Just like overwriting a file, a dialog comes up to verify the overwrite or an command option to ignore in a write script command; something similar for savepos would prevent a lot of missteps. For example, when I have two session files I am merging, the second session clobbers the first session keyframe names if they are identical, which may or may not be desirable. >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ________________________________________ >> From: Elaine Meng [meng(a)cgl.ucsf.edu] >> Sent: Friday, February 18, 2011 1:25 PM >> To: Dougherty, Matthew T >> Cc: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] animation suggestions >> >> Hi Matt, >> A few comments on your issues #1 and #3: >> >> (1) Command script execution can be aborted by pressing the Esc (escape) key, or paused/resumed with Shift-Esc. There is also a "pause" command, >> >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html> >> >> after which you could resume executing the script by pressing any key other than Esc or End, or abort execution by pressing End. >> >> (3) I'm thinking it can be done with the commands "perframe" "alias" and "2dlabels" >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> >> >> e.g. >> open 2gbp >> 2dlab create count xpos .05 ypos .05 >> alias ^framecount 2dlab change count text $1 color orange >> perframe framecount 3; roll y 1 90; wait; ~perframe >> >> I'm not sure how to exactly synchronize that with the start of movie recording, however. Maybe it would do that if the movie record command was right before the perframe command in the same line, separated by semicolon. Also, of course this is not as convenient as an automatic built-in counter. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Feb 18, 2011, at 12:21 AM, Dougherty, Matthew T wrote: >> >>> 1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script. >>> >>> 2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where & when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command. >>> >>> 3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing. >>> >>> 4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code. >>> >>> 5) I prefer to keep up with the daily builds & submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk. >>> >>> >>> thanks for the good product. >>> >>> Matthew >>> >>> >>> Matthew Dougherty >>> National Center for Macromolecular Imaging >>> Baylor College of Medicine >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Kaspersky warning
by snoze pa 18 Feb '11

18 Feb '11

While working with chimera my anti virus dtected following virus. Is it a virus or something else. http://imageshack.us/photo/my-images/651/chimeracopy.png/

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Disulfide Bond Question
by Wesley Chen 16 Feb '11

16 Feb '11

Hi, I can make the disulfide bonds show up between two cysteine resides, but I would like to draw the bond between the two alpha carbons. Right now, I can only draw the disulfide bond itself (which just shows a bar that's parallel to both cysteines) or the whole ball/stick model where all the atoms in the residues show up. I'm just trying to draw a simple bond structure between two cysteines (which is already provided in the pdb file). Thanks, Wesley

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Question
by Larry Simpson 16 Feb '11

16 Feb '11

Is there a program to convert Zeiss "zvi" files which are obtained using a Zeiss fluorescence microscope to "MRC" files (Eman files - cryoelectronmicrosopy single particle reconstructions)? I would like to be able to visualize these 3D files using Chimera. Thanks. Larry

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Labels of Metal atoms
by Michael Day 15 Feb '11

15 Feb '11

How do I make the default label for metal atoms be upper and lower case? For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc. This is true for all two letter atom names. Thanks Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------>>>

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choose a specific rotamer
by Elisabeth Ortega 15 Feb '11

15 Feb '11

Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)

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Image size reduction
by compchem compchems 15 Feb '11

15 Feb '11

Hello. Dear Chimera users, Is it possible to save part of session screen, not whole picture? I just need in high-resolution illustration. With my best wishes, Dmitry Yegorov.

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My anti-virus software detected a trojan in chimera
by Morais, Marc C. 15 Feb '11

15 Feb '11

Hi, I recently installed chimera 1.5.2 on my laptop (runs windows 7). It installed fine, but when my anti-virus software (Kaspersky) ran a scheduled scan, it claims to have found a trojan in the chimera installation. Specifically, it reports: Virus: HEUR:Trojan.Win32.Generic Location: C:\Program Files\Chimera 1.5.2\bin\ffmpeg.exe Is there a chance the program is actually infected, or is this just a false positive? Thanks, Marc

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dome/image seams
by Dougherty, Matthew T 15 Feb '11

15 Feb '11

I am getting image seams on some camera positions, attached. Any suggestions on how to minimize them? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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movie spatial sizes
by Dougherty, Matthew T 15 Feb '11

15 Feb '11

Normally I am generating movies at 640x480 or 1280x960. My graphics display is 2000x1500. I need to generate movies at 4000x4000 & 2000x2000. When I set the window size to 4000x4000 it limits it to the graphics display. How do I generate movies at the larger size? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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How to assign a unique chain ID to a receptor with two chains
by Qin Shao, Mr. 12 Feb '11

12 Feb '11

Hello I am currently using Chimera 1.5 to analysis docking simulation results from HadDock, because one of my receptor has two chains, it cannot be accepted directly. Through a communication to HadDock, I was advised that I should avoid overlapping numbering between the two chains and use a unique chain ID. Could you tell me whether I can do it on Chimera based on Windows platform, how to do it. Thank you very much. Best regards Dr. Qin Shao Montreal Neurological Institute McGill University Montreal, Canada

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Choose a specific rotamer
by Elisabeth Ortega 12 Feb '11

12 Feb '11

Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)

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zone
by Jean-Paul Armache 11 Feb '11

11 Feb '11

hello, there is a zone function for density maps+pdbs, which zones the map around the pdb in a certain radius. is it somehow feasible in chimera to do such thing with two pdbs ? what i mean is to zone a molecular model around another molecular model? (the reason for that is the speed, in which elaborate models are shown, sometimes zoning would be very useful for fast-checking). would be grateful for your help, best regards, jean-paul

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Showing actual electrostatic potential on surface
by Boaz Shaanan 11 Feb '11

11 Feb '11

Hi, Is there a way to show the actual potential value of a point on the electrostatic surface, say by pointing at it with the cursor, in an analogous way to the atom names that show up that way? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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3D with Nvideo
by Larry Simpson 09 Feb '11

09 Feb '11

I have a problem getting 3D with Chimera using a Quadro 600 video board on a Win7 64 computer. I am not sure what settings are required. Screen grabs are attached which show my current settings. Any assistance would be greatly appreciated. Larry

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Molecular weight of an EM map
by Tom Goddard 08 Feb '11

08 Feb '11

Hi Pu, Use the "Measure Volume and Area" dialog under menu Tools / Volume Data to show the volume in cubic Angstroms enclosed by your map contour surface. It will update automatically as the threshold changes. Make sure the voxel size of your map is set correctly in Angstroms because the reported enclosed volume uses that. That is set in the Volume Viewer dialog under the Coordinates panel. To estimate molecular weight from the volume you could use an approximate value for globular proteins from the literature of 1.21 cubic Angstroms per Dalton (Harpaz 1994). http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… Tom > Hi Tom, > > I have a question to ask you. > > I'm working on a 3D EM map from single particle reconstuction using Chimera. I > would like to know the total volumn of this 3D model or its molecular weight > when I change thresholds. How can I do it or where can I find this value? > > Best regards > > > Pu Qian

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Unrecognized command: "source"
by Pam Wang 08 Feb '11

08 Feb '11

Hi, I've just downloaded your program and was trying to run some alignments between two peptides. However, whenever I type in the command "source", I keep seeing the following error message: unrecognized command: "source" Could you please help me? I am able to run all the other commands, I just don't know why "source" is not recognized. Thank you, Pam Wang

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Script for positioning particles according the coordinates.
by Alexander MYASNIKOV 08 Feb '11

08 Feb '11

Dear colleagues, I would like to fit about 300 particles inside of the map according to it coordinates (X,Y,Z) what I have found before. Is it possible to make this procedure automatically, such that program would load one particle, shift it according to its coordinates (change pixel size if necessary) and so on? Thank you in advance, Alexander

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findclash "batch" calculations
by Elaine Meng 07 Feb '11

07 Feb '11

On Feb 4, 2011, at 2:51 AM, Julien wrote: > Hi Elaine, > I would like to find clashes between a ligand and a protein. I have around 100 000 poses of this ligands. > The information to get the poses are at the moment saved in a pdb file. Indeed three pseudo atoms are used to place the ligand in the correct position using the command match. > > The workflow would be the followin: > open ligand > open protein > open pseudo.pdb > > match ligand position1 > findclash > match ligand position2 > ... > > First, this is very slow, even in batch mode. Maybe you know a better way to do that. > Second chimera does not open more than 9999 residues, the pseudo pdb have nearly 100 000 residues. Is there a way to get around that. > > I guess the routine findclash calculates all distances brutally and compare them to a threshold. > many greetings > Julien Hi Julien, Findclash does calculate distances between atom centers, but the cutoff parameter is compared to "overlap" between the VDW spheres -- in other words, smaller atoms must be closer together than larger atoms to be considered overlapping or clashing. The output information (optional) includes both the center-center distances and the overlaps, however. You can limit the calculation to only certain atoms. There are also options to control cutoff and other settings. Details are here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> If you are really just using "findclash" without arguments, that would look at the whole structure and take more time than necessary. For example, if your ligand is model #0 and the protein model #1, one way to limit the calculation to only clashes between them and send info to the Reply Log is: findclash #0 test #1 log true Otherwise, I'm not an expert on any large-scale calculations or how you might optimize the procedure for large sets of atoms, so I'm CC-ing this question to the chimera-users list. (It is generally better to send Chimera questions to this list rather than to me personally.) The other users or developers may have good ideas. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Fixing registration for older versions of Chimera
by Eric Pettersen 07 Feb '11

07 Feb '11

Hi everyone, About 10 days ago I sent mail about upgrading to 1.5.2 to fix Chimera registration problems and promised a fix for older versions soon. That fix is now available from this page: http://www.cgl.ucsf.edu/chimera/fixreg/ It involves running a script on that page or, for the slightly paranoid cautious among us, downloading two files and putting them in your Chimera distribution manually. Thanks for your patience. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Rotamers
by Angelica Nakagawa Lima 04 Feb '11

04 Feb '11

Hi I can get the rotamers if I use the graphical version (when I click in tools -> Structure Editing -> rotamers). But I would like to do same thing with the comands. I used the comand swapaa (swapaa ile :10.a) and I write the pdb with the ile's rotamer (the most probable), however I would like to write the pdb file with the second most probable rotamer too. How do I do this? Thanks Angelica

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rotamers
by Ricardo Silva 04 Feb '11

04 Feb '11

I am using chimera program to view the rotamers list of pdb archive. I have proceeded from the following form: first I open an archive for chimera, later go to tools menu and alow: Structute Editing > Rotamer, after that i chose* rotamer type* and* rotamer library* then select aply and chimera display rotamers values and its respective probabilities. My objective is to save the rotamers list in an archive. Would like know how as can I make these procedures using the chimera commands. Thanks Ricardo

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