- 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

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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

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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

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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

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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."

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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.

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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.

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error message upon registration
by Boaz Shaanan 26 Jan '11

26 Jan '11

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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

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