- Chimera-users - RBVI Mailing Lists

Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 01 Mar '11

01 Mar '11

Hello, I have problem with Nvidia Quadro FX 880M and Stereoscopic view. When I switch the stereoscopic view on in Chimera it gives me following error: stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I have installed the Quadro drivers version 259.57 in Windows 7 64bit. And separate 3D driver for Quadro. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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chimera ?
by Alexander Spyros Maris 01 Mar '11

01 Mar '11

Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks! -- Alex Maris

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Internal water molecules
by Beale, John 28 Feb '11

28 Feb '11

Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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hem group
by "dr. R�szer Tam�s" 28 Feb '11

28 Feb '11

Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas

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How to
by M. Amin Arnaout 28 Feb '11

28 Feb '11

I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or CA of a residue while ribbon is also displayed. Could do that in the earlier version. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] [chimera-dev] clashes and contacts with hidden models
by Elaine Meng 28 Feb '11

28 Feb '11

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote: > > I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? > Hi Elisabeth, With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like findclash #1 test #2 [other options] Another example: findclash ligand overlap -0.4 hb 0 test aromatic Use command "help findclash" to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> This is more of a chimera-users(a)cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list. 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

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suggestion: sym option
by Dougherty, Matthew T 25 Feb '11

25 Feb '11

add an SYM command option to specify the model number of the resulting model Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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morph shape/bild objects
by Do-Nyun Kim 25 Feb '11

25 Feb '11

Hello, I'm using shapes in bild format to make spheres and cylinders in Chimera. Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation? Thanks you. Best regards, Do-Nyun Kim.

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Chain/Structure ID as label
by Berhane Temelso 25 Feb '11

25 Feb '11

Hi, I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files and tile them for analysis. It would be great to label each cluster/model with its chain ID or file name. Labeling them using the 2Dlabel command is inconvenient especially when I have a large number of models. Is there an easy way of doing this? Thanks in advance. Berhane

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Inter-helical angle?
by Brian Cannon 24 Feb '11

24 Feb '11

I need to calculate the angle between two helices in a protein. Do you have any instruction about how I could go about doing this? Any help would be greatly appreciated. Thanks! Brian

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color key creation
by Bala subramanian 23 Feb '11

23 Feb '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have opened two pdb files A and B. I also opened two attribute files corresponding to A and B and colored the ribbon based on the attribute. I want something like the following A B Colorkey 1 Colorkey2 My problem is creating the individual Colorkey. I chose model A (in the Depiction-> render by attribute -> create color key ) and created Colorkey1. When i did the same for model B and use my mouse for colorkey2 creation. Colorkey1 is deleted and Colorkey2 is created below the model B. Is it a bug. Precisely, if i hve to create two Colorkeys corresponding to two different models, how can i do that ? Thanks, Bala

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X,Y,Z coordinates in GUI
by Sujata Sovani 23 Feb '11

23 Feb '11

Wondering if it is possible to see the X,Y,Z coordinates of a particular atom in the GUI using a command? Thanks, Sujata

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need coordinates from volume data
by Terry Lang 23 Feb '11

23 Feb '11

Hey Everyone, I'm am trying to do some unorthodox analysis of volume data using a script. As part of the analysis, I need to access the x,y,z coordinates of each of the points of a ccp4 map. How would I go about that in Chimera scripting once the data is read in? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Displaying double-bonds of small molecules
by Rocco Varela 23 Feb '11

23 Feb '11

How do I display double-bonds of small molecules in Chimera?

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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 17 Feb '11

17 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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