- Chimera-users - RBVI Mailing Lists

3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

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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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dome/image seams
by Dougherty, Matthew T 14 Feb '11

14 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 14 Feb '11

14 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 11 Feb '11

11 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 10 Feb '11

10 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 10 Feb '11

10 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 03 Feb '11

03 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 03 Feb '11

03 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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surface hydrophobicity display
by Elaine Meng 03 Feb '11

03 Feb '11

Hi Sumitro, I did a little more digging for related information and thought I would share -- however, none of these methods are available in Chimera currently. Miguel Ortiz Lombardia has pointed out that the GRID program calculates a hydrophobic potential, and sent us the following links: <http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html> <http://www.moldiscovery.com/docs/vsplus/grid.html> -- the following web server sounded promising, but apparently no longer exists: PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG. Bioinformatics. 2009 May 1;25(9):1201-2. <http://www.ncbi.nlm.nih.gov/pubmed/19244385> -- the following paper discusses what surface properties of the receptor correlate well with the types of nearby ligand atoms. If I understood it correctly, they looked at how successfully Coulombic electrostatic potential and the gradient in that potential can be used to identify hydrophobic areas of surface (areas that bind hydrophobic atoms in the ligand). Both were somewhat successful, but even better was a simple definition of hydrophobic surface as the part of the surface that is not close to hydrogen-bonding groups. This paper is fairly old and the data set of ligand/receptor structures small. Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design. Bohacek RS, McMartin C. J Med Chem. 1992 May 15;35(10):1671-84. <http://www.ncbi.nlm.nih.gov/pubmed/1588550> -- then there are some other complicated functions based on molecular fragments and distances among them and to the molecular surface: A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces. Heiden W, Moeckel G, Brickmann J. J Comput Aided Mol Des. 1993 Oct;7(5):503-14. Estimating and representing hydrophobicity potential Fauchere et al. Journal of Molecular Graphics Volume 6, Issue 4, December 1988, Pages 203-206 If I understood correctly, these have many parameters and the functional form is not simple. It would not be straightforward to put them into Chimera. Finally, I also saw that the program MDL Chime has something called hydrophobic potential display, but I couldn't find a description of how it really works -- it might just be coloring whole amino acids by hydrophobicity value like Chimera does now, or atoms based on element. 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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rotamers
by Ricardo Silva 02 Feb '11

02 Feb '11

Chimera can be used to get rotamers from a selected residue of a given structure of protein and show such rotamers in a specific archive. I would like to know how to do it using a script(line commands) Thanks Ricardo

1 0

rotamers
by Ricardo Silva 02 Feb '11

02 Feb '11

I am working in the development of a program that I need the possible rotameros (of one the 5 possible rotamers) for a set of amino acids and I would like to know as chimera can make this using the command line. Debtor, Ricardo

3 2

rotamers_library
by Ricardo Silva 01 Feb '11

01 Feb '11

I have a archive .pdb and I woul like to obtain rotamers library using command Thanks Ricardo

2 1

exporting the 2drms values
by Bala subramanian 31 Jan '11

31 Jan '11

Friends, I used Ensemble match command to calculate the 2rmsd of multiple pdb files concatenated in a single pdb file. I would like to know if there is any way to save the values (as a matrix). Precisely how to output the ensemble match values. Thanks, Bala

2 3

Surface electrostatic and hydrophobicity.
by Sumitro Harjanto 28 Jan '11

28 Jan '11

Hi elaine, I've a few questions to ask about colouring surface by electrostatic potential and hydrophobicity: 1. I understand that I can use render by attribute to show surface hydrophobicity. But because it's a residue attribute, any surface of the same residue will be getting the same colour. Is there a way to calculate the surface hydrophobicity based on atoms in the vicinity instead of simply using the residue hydrophobicity values? 2. Because I have problem installing delphi, I have resorted to using the coulomb surface colouring tool. How different is this from the procedure of adding hydrogen, adding charge, then render by attribute ? Will I expect to see the same result ? Thanks elaine! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

2 2

Error in SASA calculation
by Aditya Padhi 28 Jan '11

28 Jan '11

Hi Elaine, Hope you are fine. If you remember I was calculating per residue SASA using Chimera for my MD simulated protein. At that time it was working fine. But I did some more simulation run and now I want to calculate SASA for the entire trajectory but unfortunately Its showing the following error. *Error* Problem in per-frame script: IOError: [Errno 13] Permission denied: 'sas111.txt' File "<string>", line 3, in <module> See reply log for Python traceback. For your reference, I am giving the script also. It was working fine previously but with the same procedure which I followed this script is not working and showing the above mentioned error. * Script * from chimera import openModels, Molecule out = open("sas111.txt", "a") x='---------------------------------------------------------------------------------' for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: try: sas = r.areaSAS except AttributeError: continue print>>out, r, sas print>>out,x out.close() Kindly help me. Thank you. Aditya.

2 1

Chirality inversion ?
by R. Charbel Maroun 28 Jan '11

28 Jan '11

Hi everybody, Is there an easy and quick way to invert the chirality of an atom, say a Ca ? Greetings, ----------------------------------------- R. Charbel MAROUN, Ph.D., H.D.R. Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences (INSERM U894/U. Paris Descartes) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail charbel.maroun(a)inserm.fr ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

error message upon registration
by Boaz Shaanan 26 Jan '11

26 Jan '11

2 1

1.5.2 release [fix for registration problem]
by Eric Pettersen 26 Jan '11

26 Jan '11

Hi everyone, As of a few days ago, the registration-verification certificate that has shipped with every version of Chimera for the last ten years expired. Consequently, any Chimera use after that would bring up the registration-request dialog regardless of how recently that version of Chimera had been registered. On top of that, the expired certificate caused new registrations to fail, so all you good people who were trying to help us out by registering your versions after this bug appeared were stymied. We have just released Chimera 1.5.2, which has a permanent fix for this problem. You can download it from: http://www.cgl.ucsf.edu/chimera For users who prefer not to upgrade immediately, we expect to have a solution for existing older versions in a week or less. We will send another email with details when that solution becomes available. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

electrostatic potential in active site at an interface
by Boaz Shaanan 26 Jan '11

26 Jan '11

Hi I need your advice on the following: I have an active site which is located at the interface between two subunits. The cofactor in the active site makes interactions with residues from the two subunits. I have a few mutants and would like to display their effect on the electrostatic potential around the cofactor in order to explain changes in the activity of the enzyme. I have a electrostatic potential calculated both in apbs (.px) and delphi (.phi) on the basis of whole dimer structure. My first question is whether those potential maps are relevant for displaying in chimera the potential in an inner part of the protein or should I calculate the potential over the interface region that I'd like to be displayed. If the latter is correct my second question how do I get a surface (molecular or accessible) depiction of this region. I tried several options in chimera (following some examples in the gallery) but none seems to be doing it right. I probably miss something. I would be grateful for any clues on how to go about this. Thanks for your help, 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

2 1

rotation centers
by Benoit Zuber 26 Jan '11

26 Jan '11

Hi, I have a set of density maps and PDB models. I have displayed the maps side by side. Each map has a pdb model docked in it. I would like to make a movie where each map rotates around its Z axis. Each pdb should rotate around the Z axis of its respective map. I tried: set independent roll z The problem is that the center of the pdb models is not the same as the center of their respective maps. Is there a way to group one pdb with one map so that they rotate around the same center? Or is it possible to set the center of rotation of a PDB to the same value as the center of rotation of the map? Thanks in advance Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

2 2

registration
by Francesco Pietra 25 Jan '11

25 Jan '11

I have replaced previous installation of CHIMERA with chimera alpha version 1.6 (build 32272) 2011-01-06 08:36:33 GMT. I have attempted to register at the request but the answer is that no regular installation is seen. So, at any start I have to kill the request. francesco pietra

2 1

Chimera Question
by graemeg＠rci.rutgers.edu 24 Jan '11

24 Jan '11

Hello Chimera Feedback Team, For clarity and conciseness, I will jump immediately to my issue. I wish to import a CIF file of an inorganic crystal structure into the Chimera Program so that I can selectively eliminate certain atoms, and potentially create a video similar to one of the examples given on the website with a rotation and zoom into the meat of the structure. The file I import (.CIF) should have the proper symmetry group listed in addition to the lattice parameters of a unit cell, but when I try to generate a unit cell, the space group, cell size, and cell angles sections are blank, and therefore no copies can be made. Also, the viewing options give a choice between part ball and stick, part full atom, and essentially nothing else even with selecting the different presets. I know I am not working with PDB files but if there is anything in there that you could help me with, I would greatly appreciate it. Sincere Thanks, Graeme Gardner Graduate Assistant Rutgers University Department of Chemistry and Chemical Biology

3 2

selection (from distance) among PDB files after docking
by Damien Larivière 24 Jan '11

24 Jan '11

Dear all, I have numerous PDB files resulting from a docking run. From crosslinking experiments, we know here that one way to select among all the solutions is to identify the PDB files for which the distance between some residues of interest is lower than a specific value: distance between Res 246 in chain B and Res 131 chain C < 17 A distance between Res 162 in chain B and Res 135 chain C < 24 A The two constraints must be respected. So, is it possible to write a script which: - opens one by one the pdb files, -calculates the two distances for the current pdb file, - send in the reply log the name-number of this PDB file if it respects the two constraints? Then, I would just have a look to the reply log in order to know the pdb files to study in depth. Many thanks for your help Damien

3 4

Re: [Chimera-users] font size in pull-down menus
by Greg Couch 24 Jan '11

24 Jan '11

The font size of the menus matches that of other applications on Windows. To change the size, bring up the Display Properties dialog (right-click on background, or via the Control Panel), switch to the Appearance tab, and change the font size, then Apply to see the change. If you only want to change the menu font size and leave the fonts alone (e.g., the window names and the names of icons), you can click on the Advanced button, select the Menu item, and change the font size. -- Greg On 01/24/2011 05:56 AM, Boaz Shaanan wrote: > Hi, > > Is there a way to change the font size of the pull-down menus? For > some reason on the Windows (XP) v.1.5.1 they seem smaller to me. > Nothing in terms of graphics (or my eyesight) has changed since I > upgraded to 1.5.1 recently. > > Thanks, > > Boaz > > Thanks, > > 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 >

1 0

rotate command
by Alexandra Deaconescu 24 Jan '11

24 Jan '11

Hi everyone: I am sure this can be done in Chimera, but I just could not find the proper command - I want to simply rotate a pdb file by let's say 90 degrees. Now, if I want to also rotate a map (so both map and pdb at the same time), what would I use? Can anyone help? Many thanks!!! Bests, Alex Alexandra Deaconescu, Ph.D. ----------------------------------- Research Associate, HHMI c/o Grigorieff Laboratory Brandeis University http://people.brandeis.edu/~deacona For mail: Brandeis University 415 South St., MS 029 Rosenstiel Center Waltham, MA 02454 For packages (FEDEX): Brandeis University 415 South St., Kalman Receiving Dock Waltham, MA 02454

2 1

how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

2 4

Display only selection
by Damien Larivière 20 Jan '11

20 Jan '11

Dear Chimera team, I'm identifying a complex between two proteins thanks to crosslink data. I have the following questions: 1/ I would like to select two residues that belong to two different chains and highlight them in the viewport. By using the sequence tool and then ctrl/shift+drag, I can select two residues (ex: 45 and 246 of chain A), they are highlighted in the view. But when I operate this way with res 45 of chain A and res 246 of chain B, only one remains highlighted in the view port. One way to sort this out would have been to rename all the chains with the letter A. But once the residues are highlighted, I have to measure the distance between them, then to make one chain active and then to move it and try to fit crosslink data (I hope I'm clear:-\ ). Is it possible to directly select and highlight in the viewport residues of interest belonging to different chains? 2/ Supposing that I can select and highlight in the viewport residues of interest belonging to different chains: How can I display only them in the viewport (and hide all the others)? The technical goal behind these questions is to better appreciate visually the distance between residues of interest and, thanks to the distance tool, to move one protein with respect to the other and fit crosslink data. Many thanks for your help. Damien

2 1

Chimera 1.5.1 on CentOS 5.5
by Yohei Norimatsu 18 Jan '11

18 Jan '11

Hi all, I just installed the latest version of Chimera (1.5.1 x86_64) on CentOS 5.5. I'm having a problem with MSMS surface representation. It doesn't show the surface for all the atoms and it just looks messed up. I installed the same version of Chimera on RedHat Linux 5 and it works without any problem. I don't know what the problem is. Does anyone use Chimera on CentOS? Any comment is appreciated. Thank you! Yohei

2 1

TZD Tautomer Distributions
by Nancy 17 Jan '11

17 Jan '11

Hi All, For pioglitazone, are the two tautomers depicted in the attached figure the major forms at pH 7.0? Also, are there any published articles, or other evidence that would confirm that this is indeed the correct tautomeric distribution at pH 7? Thank you, Nancy

2 1

Fwd: distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Hi everyone, As explain in the Chimera user guide, I used the command such like distance #0.2:246@N#0.5:131@N to measure the distance between two atoms of interest. To be more explicit regarding my first email, it was necessary to re-edit the pdb file and to assign a model number to each chain. In the example above, the chain B is named model 2 (then model 0.2 in Chimera) and the chain D is named model 5 (then model 0.5 in Chimera). It works fine but I suppose that there is a simpler and more direct way to specify the chain in the command? Many thanks Damien -------- Message original -------- Sujet: distance between 2 residues Date : Mon, 17 Jan 2011 18:09:11 +0100 De : Damien Larivière <damien.lariviere(a)fourmentinguilbert.org> Pour : chimera-users(a)cgl.ucsf.edu Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

2 1

distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

1 0

Cavities
by Beale, John 12 Jan '11

12 Jan '11

Is it possible to find cavities in a protein structure using Chimera? Thanks in advance! 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>

2 1

Tautomer Prediction
by Nancy 11 Jan '11

11 Jan '11

Hi All, Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57 (see attached "Figure_1.gif"). Therefore, the predominant species at pH 7.0 predicted by MarvinSketch is the one depicted in "Figure_2.gif". The different tautomeric forms predicted by MarvinSketch are shown in "Figure_3.gif". Can anyone explain where these predictions come from, and if they are correct? Also, are there other programs that can accurately predict tautomeric forms? Thanks, Nancy

2 1

Pioglitazone Tautomers
by Nancy 10 Jan '11

10 Jan '11

Hi All, I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I have attached a figure depicting several of them. Which tautomer would be dominant at the physiological pH of ~7.0? Also, are there any software programs that can predict which tautomer would be correct? Thanks in advance, Nancy

2 1

Morphing surface
by Sumitro Harjanto 05 Jan '11

05 Jan '11

Hi elaine, Thanks for the prompt responses on earlier queries. I have one more question: Is it possible to morph between 2 surfaces? Basically, I would like to show the effect in the surface contour due to a residue change. Thanks, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

2 2

Amber trajectory rmsd
by George Tzotzos 05 Jan '11

05 Jan '11

I'd be grateful if you informed if there's a way one can plot protein backbone rmsd fluctuations of trajectories. I checked file:///Applications/Chimera.app/Contents/Resources/share/chimera/helpdir/ContributedSoftware/movie/movie.html#rmsd I may have missed the salient points. Many thanks in advance George

2 1

Togl patches?
by Clifford Yapp 05 Jan '11

05 Jan '11

Hi! I recently learned that Chimera has produced some patches to the Togl widget that allow it to work with Cocoa based Tk: http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/foreign/Togl Are these updates available under Togl's current license or are they restricted by the Chimera license? Thanks, CY

3 2

Enabling multithreading in chimera
by Akshaykumar Ganguly 05 Jan '11

05 Jan '11

Dear Sir / Madam, I use chimera 1.5 regularly for protein studies on a Quad core machine with Nvidia graphics running Ubuntu. However, the application does not support multi-threading and hence, runs quite slow. Is it possible to enable multi-threading in the existing release or will such a version of chimera be released in the near future? Regards, Akshay Kumar Ganguly Research Fellow, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India

2 1

retrieving assigned color and ribbon thickness
by Sumitro Harjanto 05 Jan '11

05 Jan '11

Hi Elaine, I'm wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what's the RGB value I've assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

3 3

bond rotation
by Elaine Meng 05 Jan '11

05 Jan '11

On Jun 25, 2010, at 10:20 AM, Watson, Lisa wrote: > Hi Elaine, > I have changed several nucleotide bases in the DNA structure I am working with so that I can model in cytosine methylation. Is there a way that I can rotate the changed bases so that they are aligned to base-pair properly? > Thanks for your help! > -Lisa Hi Lisa, Sure, you can interactively rotate bonds. If you Ctrl-doubleclick a bond it should show a little menu where one of the choices is to rotate that bond. After you activate the rotation, the "adjust torsions" dialog will appear, which includes various ways to rotate the bond. You can have several rotatable bonds at the same time. Here is more about Adjust Torsions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> Also, the tutorial "Structure Comparison and Analysis" includes measuring distances, finding H-bonds and clashes, and rotating bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> 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

4 6

Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

4 3

Adjusting the quality of surface while preserving other settings
by Sumitro Harjanto 04 Jan '11

04 Jan '11

Hi Elaine, Is there a way to adjust the quality of the surface. I often use the preset publication setting to make the surface smoother before rendering images. But after activating publication quality, the speed will slow down, and I will experience lag (especially with large models) when I try to move/turn the models around. I wondering if I can toggle between 'interactive' and 'publication' quality for the surface only without affecting the background /ribbon settings..? thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

2 1

index out of range
by Francesco Pietra 03 Jan '11

03 Jan '11

Hello: Two not new questions. (1) I am trying to read prmtop/mdcrd files from Amber MD with chimera alpha version 1.5 (build 30702) 2010-06-10 23:51:24 GMT, getting "index out of range" (the files are correct, they open with VMD) MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. - HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) Traceback (most recent call last): File "/usr/local/chimera/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera/share/chimera/baseDialog.py", line 342, in command getattr(s, buttonFuncName(txt))() File "/usr/local/chimera/share/chimera/baseDialog.py", line 560, in OK self.Apply() File "/usr/local/chimera/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 72, in loadEnsemble addTrajKw=self.addTrajKw) File "/usr/local/chimera/share/Trajectory/DCD/__init__.py", line 85, in loadEnsemble ensemble = DCD(psf, dcd, startFrame, endFrame) File "/usr/local/chimera/share/Trajectory/DCD/DCD.py", line 24, in __init__ mdtMol = md.Molecule(psf=psfPath) File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py", line 356, in __init__ nrecs = int(psfrec[0]) IndexError: list index out of range IndexError: list index out of range File "/usr/local/chimera/share/Trajectory/DCD/MDToolsMarch97/md_AtomGroup.py", line 356, in __init__ nrecs = int(psfrec[0]) See reply log for Python traceback. ************************************************ (2) Although I suppose I used in the past ATOM ATTRIBUTES to display chloride anion at its standard radius in preparing figures for publication, I just get it now as a tiny dot as set by MODELLER. That with proteins without or with non-polar hydrogens. For example TER 6750 LYS A 426 ATOM 6751 Cl- Cl- A 427 -31.021 4.748 41.205 1.00 6.32 Cl TER 6752 Cl- A 427 ATOM 6753 N LEU B 1 -13.959 20.979 -35.226 1.00 63.95 N I can't remember how to specify the chloride radius in command sel :427@Cl- ************************************************ Thanks for pointing me to the correct procedure francesco pietra

2 2

query
by SURESH KUMAR 03 Jan '11

03 Jan '11

hello sir, I need to find electron density of protein, i am planning to use UCSF Chimera software for that... so please help me how to find protein electron density using UCSF Chimera thank you A.Suresh Kumar, M.Tech Biomedical Engineering, Amrita School of Engineering, Ettimadai, Coimbatore.

2 2

Re: [Chimera-users] center of rotation
by Eric Pettersen 03 Jan '11

03 Jan '11

On Dec 30, 2010, at 11:02 AM, Bill Montfort wrote: > Thanks! This works well. If there were a quicker means for > activating Set Pivot, this would be even better (e.g. keyboard or > mouse combination). Cheers! Okay, for added convenience I've put a "Set Pivot" item in the atom context menu, which you can access by control-double-clicking an atom. This is only available in the 1.6 daily build and only as of tonight's upcoming build (so 1.6 builds dated Jan 3 or later). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Mirror image proteins
by Stephen B.H. Kent 03 Jan '11

03 Jan '11

How can I invert the configuration of a pdb file to create the mirror image model of the protein molecule? Thanks, Steve Kent Stephen Kent Professor of Chemistry Professor of Biochemistry & Molecular Biology Institute for Biophysical Dynamics Mail: Gordon Center for Integrative Science, Room W204 University of Chicago 929 East 57th Street Chicago, IL 60637, USA Tel: +1 773 702 4912 Email: skent(a)uchicago.edu

3 3

Thiazolidinedione Tautomers
by Nancy 03 Jan '11

03 Jan '11

Hi All, I am performing molecular docking and molecular dynamics simulations of thiazolidinediones (TZDs) binding to the ligand binding domain of the PPAR-gamma receptor protein. The thiazolidinedione ring can exist in numerous different tautomeric states (see attached figure); is there any particular tautomer(s) that would be dominant, and thus most appropriate for docking and molecular dynamics simulations, at pH 7.4? I have read the article "Metformin and glitazones: does similarity in biomolecular mechanism originate from tautomerism in these drugs?" J. Phys. Org. Chem. 2008, 21 30–33, as a reference, but it does make it clear as to which tautomer is most appropriate for simulating binding to a receptor protein at pH 7.4. Thanks in advance, Nancy

2 1

Re: [Chimera-users] center of rotation
by Elaine Meng 30 Dec '10

30 Dec '10

Hi Bill, If command "cofr sel" is too long, you could (a) use the command "alias" to alias it to a shorter command, e.g. alias ^blah cofr sel which would then allow you to use the command "blah" or if you don't use the Command Line, (b) define your own keyboard shortcut <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accel…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accel…> However, the latter requires some Python, on which I cannot advise. Elaine On Dec 30, 2010, at 11:02 AM, Bill Montfort wrote: > Thanks! This works well. If there were a quicker means for activating Set Pivot, this would be even better (e.g. keyboard or mouse combination). Cheers! > > On Dec 30, 2010, at 11:18 AM, Eric Pettersen wrote: > >> Alternatively, you can control-click on the atom to select it and then >> choose Actions->Set Pivot in the menus to make it the center of >> rotation. >> >> On Dec 30, 2010, at 9:51 AM, Elaine Meng wrote: >> >>> Hi Bill, >>> You can use the command "cofr" with specified atoms (including "sel" >>> as the specification if the atom or atoms are selected). >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> >>> >>> There are several different rotation modes, and you can switch among >>> them using either "cofr" or the Rotation tool (under Tools... >>> Movement in the menu). >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#rotation >>>> >>> On Dec 29, 2010, at 3:55 PM, Bill Montfort wrote: >>> >>>> I'm returning to chimera after many years away and am quite >>>> impressed with the program, save for one issue: rotating about the >>>> screen center. My favorite way of viewing structures is for the >>>> rotation to be about a center of my choosing, as is common in many >>>> graphics programs (e.g. COOT). I would prefer to pick an atom on >>>> the screen and have this become the rotation center. Is there a >>>> simple way to accomplish this in chimera? A small point perhaps, >>>> but one that is frustrating for me....... >>>> >>>> Bill Montfort

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center of rotation
by Bill Montfort 30 Dec '10

30 Dec '10

I'm returning to chimera after many years away and am quite impressed with the program, save for one issue: rotating about the screen center. My favorite way of viewing structures is for the rotation to be about a center of my choosing, as is common in many graphics programs (e.g. COOT). I would prefer to pick an atom on the screen and have this become the rotation center. Is there a simple way to accomplish this in chimera? A small point perhaps, but one that is frustrating for me....... Bill Montfort

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Quiero ser tu amigo en Quepasa.com
by Sergio Garay 27 Dec '10

27 Dec '10

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average structure of superimposed models
by Sumitro Harjanto 23 Dec '10

23 Dec '10

Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an 'average' structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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[chimera-users]about "color key"
by C.J. 22 Dec '10

22 Dec '10

Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.

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CASTp .poc
by S. Shunmugasundararaj 22 Dec '10

22 Dec '10

Hi Everybody, I loaded the CASTp *.poc file in Chimera and saved as a *.py file. When I open the .py file later, I do not see the .poc details. Is it hidden somewhere or how do I get that details? I do not see the "instance" item in the Tools menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html page does not seem to have the details about that. Thanks Raj

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File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

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File conversion: strange behaviour
by George Tzotzos 22 Dec '10

22 Dec '10

Hi everybody, I'm attaching a pdb file <3og.pdb>. This file on conversion from amber11 (ANTECHAMBER) yields 3og.mol2 which Chimera renders as per snapshot below. The two big blue spheres should be oxygen atoms. Selecting the molecule and trying to colour by atom has no effect other than colouring the atoms that are adjacent to the blue spheres. Any explanation for this behaviour? Many thanks and best regards George

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Re: [Chimera-users] [chimera-dev] Coloring
by Elaine Meng 21 Dec '10

21 Dec '10

Hi Hajeung, To color all carbons green the command would simply be color green,a C whereas "byatom" means to use the built-in element coloring scheme, not a specific color <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> and @ means atom name, not element, so "@C" would only get the atoms named C (not CA,CB, etc.). General user questions should probably go to chimera-users(a)cgl.ucsf.edu (chimera-dev is for development/programming questions). 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 Dec 19, 2010, at 5:36 AM, Hajeung Park wrote: > Hello, I want to color “C” to a certain color. The manual is not very clear bout it. > My understanding is > > Color green byatom ,a @C > > But it give me error. > > Thanks.

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Curves+ graphics of DNA
by Richard LAVERY 21 Dec '10

21 Dec '10

I am trying to visualize the graphic output from the Curves+ of a DNA duplex, which consists of two smooth backbone traces linked by vectors indicating the measured widths of the minor and major grooves. In the test case shown, adding two atoms defining one such vector and a single CONECT line linking them together (see attached PDB file) leads to three new bond vectors in the representation shown below. Am I making a mistake, or is this a problem with Chimera? Richard LAVERY richard.lavery(a)ibcp.fr http://web.mac.com/laveryr/Homepage Institut de Biologie et Chimie des Protéines 7 passage du Vercors, Lyon 69367, France Tel: +33 (0)4 72 72 26 37, Cell 06 62 76 84 47

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changing HIS to HIP
by Francesco Pietra 16 Dec '10

16 Dec '10

Hello: I need to change several histidine residues (both HIS and HIE, although both called HIS) to HIP. I tried manually. In case of monoprotonation at NE2: modify structure element N bonds 3 geom trigonal connect to preex atoms color by element change modified residue's name to HIP set atom names to ND1 or retain current atom names In both cases the proton attached to ND1 takes the name "H1" instead of the expected HD1. Is that error in the above procedure or chimera bug? (chimera alpha version 1.5 (build 30702) on GNU/LINUX 32bit) Addendum: is there any other method of accomplishing the task with chimera? It is rather troublesome to go through all monoprotonated histidines of this large homomer (in different chains HIS of the same number have been differently protonated by reduce). A problem with reduce (if not my misuse of reduce) is that all histidines become monoprotonated, while the experimental pH is such that all should be diprotonated. I must add that I am bound to reduce because the program that I use subsequently goes through reduce. thanks for help francesco pietra

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selection line-width
by Daniel Gurnon 15 Dec '10

15 Dec '10

Hi everyone, Two requests that would help with interactive demonstrations to large audiences: In preferences/background, the selection mode can be "fill" or "outline". Is it possible to add a line-width option for outline? I want to increase the thickness of a selection outline to make it easier for my students to see when I'm projecting an image, but I don't want to use the fill option and lose residue color information. I suspect that's an easy fix, but this one might be more difficult: Transparent surfaces are very informative when combined with underlying ribbons or stick representations of atoms. But if a residue is visible beneath a transparent surface, selecting it (via the command line) does not show the selection outline. Is it possible to make that work? Thanks, Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] [Chimera-announce] Chimera 1.5 release
by Elaine Meng 15 Dec '10

15 Dec '10

Hi Surendra, Yes, if you are doing map-in-map fitting, it calculates the correlation values, in 1.5 and also in earlier versions. You have the choice of calculating the correlation about zero or about the mean. If you are doing atoms-in-map fitting, it does not give correlation values UNLESS you turn on the "Use map simulated from atoms" option, and in that case you also need to enter a resolution value for the simulated map. If you click the Help button on the dialog it will show the manual page with more detailed explanations, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> 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 Dec 15, 2010, at 9:33 AM, Negi, Surendra S. wrote: > Hi Elaine, > In EM fit, Is it possible to calculate the Correlation? I am using current version 1.5 of UCSF chimera. > Thank you. > Surendra > ps: the snapshot is available at : http://img221.imageshack.us/img221/2492/screenshotpt.png

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Maximum surface areas for each amino acid
by Boaz Shaanan 15 Dec '10

15 Dec '10

Hi Elaine, The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142. Best regards, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Tuesday, December 14, 2010 21:11 Subject: Chimera-users Digest, Vol 92, Issue 11 To: chimera-users(a)cgl.ucsf.edu > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Maximum surface areas for each amino acid (Tom > Goddard) 2. Center of segmentation regions (Tom Goddard) > 3. Chimera Error (Kshatresh Dutta Dubey) > 4. Re: Chimera Error (Elaine Meng) > 5. Re: Maximum surface areas for each amino acid > (Elaine Meng) > 6. 3D-Stereo. (ayassin(a)wadsworth.org) > 7. merging 3D volumes (Marlovits,Thomas) > 8. Re: merging 3D volumes (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Mon, 13 Dec 2010 18:08:11 -0800 > From: Tom Goddard <goddard(a)sonic.net> > Subject: [Chimera-users] Maximum surface areas for each amino acid > To: iropson(a)psu.edu > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4D06D18B.7040806(a)sonic.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ira, > > I don't know of any table of maximal solvent > accessible surface areas > for each residue type when bounded by glycines. Maybe > someone on the > Chimera mailing list will know. > > A Chimera Python script could run through the PDB > and accumulate > per-residue surface area statistics. One trouble with that > would be > that surface calculation fails in Chimera in some percentage of > cases > (~5%) due to numerical problems. > > Tom > > > Hi Tom, > > > > Love the software. Do you have a table for calculating the > maximum > > available surface area for amino acids eg.(Gly-Xxx-Gly) so > that I can > > get a relative percentage exposed surface area from the > calculations? > > Do you know how to find one in the literature? Has anyone > written a > > program that describes the possible surface exposure for a > residue in > > a particular secondary structure and/or a particular sequence? > This > > maximal value would certainly be different depending on the > local > > sequence and structure. For example, a residue in the middle > of a > > helix would have to be shielded from the solvent by the i+4 > and i-4 > > residues, and the size of those residues would matter. > > > > Thanks, > > Ira > > > > > > On 12/10/10 2:41 PM, Tom Goddard wrote: > >> Hi Sumitro, > >> > >> I made a Chimera video tutorial showing how to > determine which > >> residues are on the surface. > >> > >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > >> > >> Tom > >

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delete named selection
by S. Shunmugasundararaj 14 Dec '10

14 Dec '10

Hi, How do I delete the "Named selection" from the chimera file? I could not get the info from the archive or by searching the web. Thanks in advance Raj

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3D-Stereo.
by ayassin＠wadsworth.org 14 Dec '10

14 Dec '10

Hello, Will the sequential stereo work with the Nvidia 3D vision kit available with the Toshiba 3DV series laptops? if not, What would be the best option for sequential stereo? Thank You. Aymen Yassin. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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merging 3D volumes
by Marlovits,Thomas 14 Dec '10

14 Dec '10

Hi, I was wondering, whether a 3D map can be placed into a box with a user defined number or x/y/z planes ? Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file. Is this possible ? Tx for your fast answer, Best, -Thomas Thomas C Marlovits Research Group Leader marlovits(a)imp.ac.at

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Chimera Error
by Kshatresh Dutta Dubey 14 Dec '10

14 Dec '10

Dear All, When i am trying to assign partial charge on a molecule, it is giving error something like this- AttributeError: '_chimera.Atom' object has no attribute 'gaffType' File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in writeMol2 atomType = atom.gaffType I am using chimera 1.5 on linux 64-bit Kindly help to resolve this problem Thanks in advance kshatresh

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Maximum surface areas for each amino acid
by Tom Goddard 14 Dec '10

14 Dec '10

Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom > Hi Tom, > > Love the software. Do you have a table for calculating the maximum > available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can > get a relative percentage exposed surface area from the calculations? > Do you know how to find one in the literature? Has anyone written a > program that describes the possible surface exposure for a residue in > a particular secondary structure and/or a particular sequence? This > maximal value would certainly be different depending on the local > sequence and structure. For example, a residue in the middle of a > helix would have to be shielded from the solvent by the i+4 and i-4 > residues, and the size of those residues would matter. > > Thanks, > Ira > > > On 12/10/10 2:41 PM, Tom Goddard wrote: >> Hi Sumitro, >> >> I made a Chimera video tutorial showing how to determine which >> residues are on the surface. >> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html >> >> Tom

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Center of segmentation regions
by Tom Goddard 13 Dec '10

13 Dec '10

Hi Tyler, The Chimera Segger segmentation tool currently doesn't report the geometric center of segmentation regions or the principal axes. I've attached a Python script that will do that. Select the regions in Chimera then open the script (File / Open). The results will appear in the reply log (menu Favorites / Reply Log). The results are in physical coordinates (taking account of volume grid spacing), not grid index units. Tom > Dr. Meng, > > I am using Segger in Chimera and displaying the principal axes for > some of my segmentations. I am wondering if there is a way to find > the XYZ coordinates of the origin of the principal axes for each of my > segments. Is there a way to put the coordinates for these axes in a > text file? > > Thank you, > > Tyler Steele >

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Inatallation Location
by Stephen P. Molnar 13 Dec '10

13 Dec '10

Chimera 1.5 (32-bit) on OpenSuSE 64-bit v11.2 I have just installed 1.5 on my syustem.. The installer insists on an installation in /home/computation/.local in spite of my attempts to install in a location of my choice. This is rather annoying as I prefer to install software on a hard drive that will not be overwritten when I upgrade the OS. Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivarate http://www.FoundationForChemistry.com

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