- Chimera-users - RBVI Mailing Lists

Coulombic Surface Coloring
by Francesco Pietra 03 May '09

03 May '09

Hi: I would like to simply color the surface of a protein by the Coulombic Surface Coloring method. I can show the surface, have a file with calculated charges if useful, but i am unable to implement the indications below "There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category. The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP. " which tool should be opened from Surface/Binding Analysis? Of those related, I can only see Electrostatic Surface Coloring and that - in my hands - does not bring to the simple Coulombic method. Thanks for clearing francesco pietra

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recording operations
by Fajer 03 May '09

03 May '09

Dear All, Does Chimera record the "menu" selected operations that can be played back in a manner analogous to storing "command" entered operations ? I'd rather avoid having to modify python script of the stored session. Peter Fajer

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My Chimera 1.4 build 27395 is not keeping 2D Labels when saving images except if Pov-Ray tracing is turned on
by Victor Alves 01 May '09

01 May '09

Hi When I save a picture with 2D Labels, they don't show up in the saved image. I tried with different image types (jpg, tiff, png) and even a new image just with some 2D Labels in it. I don't know if this is important but all of them have a white background. The only way I managed to see the labels was to turn on Pov-Ray tracing! Any ideas? Thank you in advance Victor Alves

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Re: [Chimera-users] pivot point
by Elaine Meng 30 Apr '09

30 Apr '09

On Apr 30, 2009, at 10:51 AM, Tatyana Fedotova wrote: > Dear Mrs. Meng, > I have a question about pivot point. > Could you explain howfor example I can rotate part of a helix from a > chosen pivot point. > I fount how I can selet and move atoms. But that's not what I need. > Thanks, > Tanya Dear Tanya, I can think of two ways to move only part of a structure rather than a whole model: (a) by rotating bonds, see Adjust Torsions, where the bonds define the pivots <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > (b) with Movement Mouse Mode, which is probably what you were talking about <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.… > Although method (b) does not include control over the center of rotation (pivot point), you can set the center of rotation before using that tool. You can set the center of rotation to an atom or centroid of a set of atoms by selecting the atom(s) and using "Actions... Set Pivot" in the menu. Or, you can use the "cofr" command to do the same thing, or if you have a fairly recent version of Chimera (1.4, so a daily build), specify particular X,Y,Z coordinates as the center. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> The center of rotation set as described above also applies when you are rotating whole models. In newer versions of Chimera (1.4), the rotation commands "roll" and "turn" also allow specifying the center to use when executing that command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu rather than my personal address, unless you are describing private data. Even though I answer a lot of those messages, I might be sick, or on vacation, or not know the answer! Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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creating volume maps
by Nils Becker 29 Apr '09

29 Apr '09

Hi, I would like to use chimera for measuring the steric accessibility of particular atoms in a structure to reactive species in solution. To do that I had the following idea: 1. create a volume map which represents a solid sphere centered on the atom in question (alternatively, a Gaussian blob), with some chosen radius. 2. mask this sphere using the solvent accessible surface of the protein (for example, if the atom is at the surface and the surface is flat, half of the sphere would be cut away) 3. measure the volume of the remaining piece of the sphere. So now my question is: can this work, and how can I generate the sphere in step 1. ? thanks for any advice! Nils

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color by element
by Eric Pettersen 28 Apr '09

28 Apr '09

On Apr 28, 2009, at 3:31 PM, Thiruvarangan Ramaraj wrote: > Hi Eric, > > I have a question regarding the colouring by element option. > > If I select a surface and I go to colour and choose by element, does > it colour in any order, if so what is the order, how do i find out > what element is given what colour. > > Thanks for your time > > Thiru Hi Thiru, I'm not sure what you mean by "does it colour in any order", but the colors assigned to each element are described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortables.html#by… and how you can change them is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/colordef.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Problem recording raytraced movie
by Tom Goddard 28 Apr '09

28 Apr '09

maya shcushan wrote: > Dear Tom, > Thanks, this was very helpful... > I have a new question: I want to make a simple movie in which the molecule > rotates. Using the commands script I found on the internet, the movie is of > very low quality (attached). Moreover, running it with windows media player > shows the opening in the script, embedded in the movie. This were the > commands: > > "movie record > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > > I want to record the same movie in good quality, like the pictures I get > with pov-raying. I tried running: > "movie record raytrace true > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > But it falls all the time. > > I looked in the internet for scripts but didn't find an answer. Can you > please help me to create a simple script in which the molecule rotates and > presented in ray-tracing and high quality? > > Thanksm > Maya > > Hi Maya, In Chimera 1.3 before the movie encode command you need the command "movie stop". movie record raytrace true turn y 3 150 wait 150 movie stop movie encode mformat avi output spin.avi bitrate 4000 Otherwise it keeps on recording frames forever. In Chimera 1.4 (daily builds) this is unnecessary and your original script works correctly because in 1.4 movie encode does a movie stop implicitly. Tom

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measure
by julien(GWDG) 28 Apr '09

28 Apr '09

Dear all, I have the last vesion of chimera 1.4 (27371) under a linux machine. I want to use the measure function. I have two models. The difference between this 2 models is a 5 degree rotation around the x axis. >> matrix rotation #1 #0 >>reply in the log Position of test.pdb (#0) relative to test1.pdb (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 I think the command does not work in this version (if I misunderstood the command please tell me as well). It always give me the same answer for any different models I did try. Since I have to ask my admin each time I want to install something, could you just tell me in which version of chimera this command will work. Many many thanks. best Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

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noeshow
by Randazzo Antonio 27 Apr '09

27 Apr '09

Hi all, I am new of chimera and I am trying to display the NOEs that I have used in my calculations along with the structured I have obtained. With my big surprise I have discovered that in a previous version of the program (MIDAS) this was possible (by the command NOESHOW), but it seems that this features is not supported in this version of the program. Do you have any clue in how to resolve this? Is there a workaround or I have to use another program? If this is the case, which program (sometimes I need to display an Amber restraint file or a Discover restraint file). Thanks in advance for your help

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Stereo Monitors
by hsosa＠aecom.yu.edu 24 Apr '09

24 Apr '09

Hi, I was wondering if chimera work with one of these stereo monitors that split the image into two opposite circularly polarized images (e.g. MIRACUBE G170S) so that you can use cheap passive glasses, similar to the disposable ones used in some movies. Also I'll be interested If anybody has experience using these monitors. I think they are under $1000 now for a 17' monitor Best Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] Color Key
by YangMingjun 24 Apr '09

24 Apr '09

Dear Professor, Thanks so much. It works well now. Mingjun >Hi Mingjun, >your version is very, very old. For Color Key you need at least the >last production release, version 1.3 from 2008. If you go to the >Chimera home page, > >http://www.cgl.ucsf.edu/chimera/index.html > >there are download links on the left, "production release" for the >most recent production release, and "daily builds" for even newer >ones if you want the things that are described in the "what's new" >link right next to "daily builds." There are release notes for each >version that say what is new in that version. Color Key was a new >feature in the 1.3 release. > >Your version is so old it might not even have those color squares in >the Model Panel that I mentioned before! >Best, >Elaine > > >On Apr 23, 2009, at 6:45 PM, YangMingjun wrote: > >> Dear Professor, >> >> Thanks very much. >> I can't find the Color Key icon in my installed Chimera >> following the step in the link. Is it due to the version I am using? >> I am using Windows os and chimera-1[1].2422-win32.exe >.

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Re: [Chimera-users] Color Key
by YangMingjun 23 Apr '09

23 Apr '09

Dear Professor, Thanks very much. I can't find the Color Key icon in my installed Chimera following the step in the link. Is it due to the version I am using? I am using Windows os and chimera-1[1].2422-win32.exe Mingjun >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >> 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >.

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Re: [Chimera-users] Chimera-users Digest, Vol 72, Issue 26
by YangMingjun 23 Apr '09

23 Apr '09

Sorry that I send my question to you directly by replying your last response in the mailing list. I have sent one to the chimera-users(a)cgl.ucsf.edu Mingjun >Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Color Key (Elaine Meng) > 2. Re: Color Key (Elaine Meng) > 3. Re. Volume squeeze (Priyaranjan.Bhakat(a)csiro.au) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 23 Apr 2009 09:32:05 -0700 >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Subject: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA(a)cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >Dear Mingjun, >Oh, now I see -- you want a color key! Yes, you can do that in >Chimera: choose Tools... Utilities... Color Key. In that dialog you >can set the colors and the value labels. You can click and drag with >the mouse to draw the key in the Chimera window. If you need more >text, you can add it with 2D Labels, which is another tab on the same >dialog as Color Key. > >Here is the full description: ><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >2dlabels.html#colorkey> > >and here is an example image with both Color Key and 2D Labels: ><http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> > >You would add that stuff while you are still in Chimera, and then >when you save the image, it will be included. You might also be >interested in this page on "tips" for making images: ><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > >On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: > >> Dear Professor, >> Thanks so much. I am the first time to use Chimera so I am sorry >> that if my questions seem to be too simple... Sorry that I didn't >> describe my question clearly in last post. >> I had got the figure of 20 frames which are colored by using the >> command "rainbow models red, blue". Then I saved the figure with >> the file name a.png. Now I'd like to use the color range to denote >> each frame in the paper, e.g. color range from red to blue gradual >> changes corresponds to colors used by model 1 to 20 in the saved >> figure. Since I don't know what is the name it is should be called >> in English language, I send you an example in the attachment. >> Many thanks. >> Mingjun > > >------------------------------ > >Message: 2 >Date: Thu, 23 Apr 2009 10:34:06 -0700 >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Subject: Re: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users BB <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065(a)cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >> 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >------------------------------ > >Message: 3 >Date: Thu, 23 Apr 2009 12:07:33 +1000 >From: <Priyaranjan.Bhakat(a)csiro.au> >Subject: [Chimera-users] Re. Volume squeeze >To: <chimera-users(a)cgl.ucsf.edu> >Message-ID: > <DB072BAE3B16E3488CEF9F65E6D35B3F2E3CF42A(a)exvic-mbx01.nexus.csiro.au> >Content-Type: text/plain; charset="us-ascii" > >Hi, >I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. >Alternatively, what the best way to overlay and compare two volumes. >Thanks in advance for any clue, >Priya >

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Re. Volume squeeze
by Priyaranjan.Bhakat＠csiro.au 23 Apr '09

23 Apr '09

Hi, I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. Alternatively, what the best way to overlay and compare two volumes. Thanks in advance for any clue, Priya

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transition command
by Eaazhisai Kandiah 23 Apr '09

23 Apr '09

Hi, I found the answer for the transition command. Actually It has been discussed in the forum before. It is in the Experimental features site and under Animation commands. Will try that. Sorry about repeating the question. Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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transition command
by Eaazhisai Kandiah 23 Apr '09

23 Apr '09

Hello Developers, I would like to use the transition command to travel through the radius of an icosahedron surface. The builds and release I have, do not recognize the command 'transition'. Could you please tell me which version/build of chimera I should be using for this command? Thanks a lot, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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Re: [Chimera-users] (no subject)
by YangMingjun 23 Apr '09

23 Apr '09

Dear Professor, Thanks so much. I am the first time to use Chimera so I am sorry that if my questions seem to be too simple... Sorry that I didn't describe my question clearly in last post. I had got the figure of 20 frames which are colored by using the command "rainbow models red, blue". Then I saved the figure with the file name a.png. Now I'd like to use the color range to denote each frame in the paper, e.g. color range from red to blue gradual changes corresponds to colors used by model 1 to 20 in the saved figure. Since I don't know what is the name it is should be called in English language, I send you an example in the attachment. Many thanks. Mingjun >Dear Mingjun, >After the rainbow-coloring, open the Model Panel (under Favorites in >the menu). There it will show the color for each model in a square. >If you click any of those squares, called "color wells," it will >bring up the color panel (Color Editor) set to that color. >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > >On Apr 22, 2009, at 6:54 PM, YangMingjun wrote: > >> Dear Professor, >> Thanks very much for your detailed instruction. >> If I use rainbow models red,blue >> then can Chimera produce a color panel to denote the colors used? >> Thanks >> Mingjun >> >.

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(no subject)
by YangMingjun 22 Apr '09

22 Apr '09

Dear Professor, Thanks very much for your detailed instruction. If I use rainbow models red,blue then can Chimera produce a color panel to denote the colors used? Thanks Mingjun > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Mole… > You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.ht… > Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors > For asking Chimera questions, please send mail to chimera-user at cgl.ucsf.edu and not to me directly, unless you are sending private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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[Chimera Help] Multiple Instances
by cdlau＠ucsd.edu 22 Apr '09

22 Apr '09

Dear Madam/Sir, I found this from a response 5 years ago in 2004 > As it works now, if you wish to send commands to an already running > Chimera, you cannot specify which instance of Chimera. So it is not > possible to communicate with multiple instances of Chimera as you might > want to support multiple web sessions. Dan Greenblatt may have ideas > for addressing this. > > Tom I was wondering if this is still the case. I am interested in running multiple instances of Chimera on a Tiled Wall Display and have global control over all the instances. Does anyone have any suggestions or resources for me to look into? Thanks in advance, Christoper

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Re: [Chimera-users] Straighten a helix
by Elaine Meng 22 Apr '09

22 Apr '09

Hi Francesco, You don't have to give the atom names for each residue, e.g. how about match #0:24-30 #1:24-30 (assuming these residues have equal numbers of atoms with the same names in the two structures) or match #0:24-30@n,ca,c,o #1:24-30@n,ca,c,o or match #0:24-30@ca #1:24-30@ca You may want to try the "iterate" option of the match command. You could use matchmaker instead of match, but that would use the whole chain rather than specific residues, so I doubt it fits your situation. Here is a discussion of the different ways to match things in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 22, 2009, at 10:32 AM, Francesco Pietra wrote: > Elaine: > I have found a way to get a nearly perfect alpha helix from what was a > bent alpha helix by imposing the phi and psi angles where they were > out of the norm. However, both the barycenter and the orientation of > the rectified helix have changed, so that it does no more fit its > partners. > > What I would like to do is using the Chimera "match" command to > superimpose the rectified helix to the bent helix, then remove the > bent helix and save pdb. Surely clashes will be there but perhaps not > so many to hinder MD. Is there a short command to tell to Chimera to > do the job without having to list atom per atom. The helix is long and > trial and errors will be many...it is not laziness alone. > > Or is anything better in Chimera than the match command? > thanks > francesco

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Question about Chimera
by YangMingjun 22 Apr '09

22 Apr '09

Dear Professor, I am going to use Chimera to plot 20 molecular frames (saved in 10 files with the file name frame_$n.pdb) in one figure and have a question about the color scheme. I'd like to check the conformational changes from frame 1 to frame 20. Can you please tell me how to color the frames, e.g. with gradual change of each frame in color from red to blue ? Does Chimera adopt a default method to color an ensemble of structures when loaded? Thanks so much. Mingjun

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Re: [Chimera-users] atomic fluctuations
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 10:26 AM, Bala subramanian wrote: > Dear Elaine and Pett, > > Greetings. I have a matrix of atomic fluctuations, is it possible to > map it on to the structure using chimera. Say i would prefer to color > differently all atoms having a fluctuation of more than a threshold. > Similarly if i give a matrix of correlations, i should color > differently those atoms which are highly correlated. > > Thanks, > Bala Dear Bala, To do this you would create an "attribute assignment file" (a simple text format) with the values and read it in with Define Attribute (or command "defattr"). That will assign the values to your structure as an "attribute." Then you can show the values of your new attribute with colors, etc., and select atoms based on those values, and use them in command-line specifications, just like any other attributes (bfactor, kdHydrophobicity, etc.). This is exactly what you need for the fluctuation values. Showing the correlation would be more complicated, because attributes are properties of atoms and not atom pairs. You could assign each "row" of your correlation matrix as a different attribute with a different name. Define Attribute and the concept of "attributes": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Attribute assignment file format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Render/Select by Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html > Please send questions about Chimera to chimera-users(a)cgl.ucsf.edu and not to our personal addresses, unless you are sending private data or information. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Rainbow-coloring
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 9:13 AM, YangMingjun wrote: > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Mole… > You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.ht… > Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors > For asking Chimera questions, please send mail to chimera-user(a)cgl.ucsf.edu and not to me directly, unless you are sending private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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surface failures
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 1:26 AM, Cédric Govaerts wrote: > Hi Elaine, > Here is my problem, seems like I cannot compute these surfaces on > some PDBs > and receive the following message in the Reply Log: > > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1 > Calculation of some surface components failed (code 5). > Falling back to single-component calculation. > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 > Surface calculation failed, mscalc returned code 5 > > I attach the PDB so you can try it for yourself. Hi Cedric, This is an uber-common problem in Chimera due to the numerical failure of the embedded MSMS code on some structures. There are many workarounds that are slight changes to the surfacing parameters or VDW radii, but it is an art rather than science to find them -- just requires trial and error and typically is different on different machines. For example, on both my mac 10.4 laptop and mac 10.5 desktop machines, I just opened your structure and showed the surface without any problems or doing anything special. Because of the MSMS problems, we have been working for many months on code to replace it. We are hoping to have our own surfacing code ready for the next production release. In the meanwhile, I will briefly summarize some things to try (but be aware they can affect your surface area results): - if your structure has multiple chains and you don't mind having a separate surface for each chain, use the "split" command to split it into separate models before surfacing - before creating the surface, adjust related parameters in the New Surfaces category of Preferences (under Favorites). For example, you can adjust vertex density and/or probe radius. if you only care about the main outer surface and not interior bubbles you can turn off "show disjoint". Actually you might prefer not to have interior bubbles included in your results. Sometimes the components that fail are just those interior bubbles, and "single-component calculation" as mentioned in your message of the main outer surface still works. However, in your case both failed. - slightly change VDW radii, e.g. with command "vdwdefine +.05" (you can put them back to default with command "~vdwdefine") Here are several previous posts on this issue: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/ 002954.html> > >> ("component") are reported in the Reply Log. At the same time, it >> creates atom and residue attributes named areaSES and areaSAS. > > Hum, anyway I can retrieve such per residue information ? > Maybe in a text file or something ? > Just to make sure, I can compute the SAS for each atoms based on the > complete structure (including sidechains) and then obtain the > individual > values for each atoms (say backbone nitrogens in this case.) You can save the attribute values (atom or residue attribute named areaSAS or areaSES) to text files using the Render by Attribute dialog's File menu. I will mail you the text file for atom attribute areaSAS for your structure in a separate message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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delete model
by Damien Larivière 21 Apr '09

21 Apr '09

Dear Chimera team, I have used the multiscale model for generating a surfacic model of (pdb) file 1YAU.mmol (from pdb sum). Two models are displayed (see attached image): one is an all-atom model and the other is the surfacic model. I would like to know : - how to delete the all-atom model in order to export in the vrml format only the surfacic model (the two-model scene is fast for exporting but very long for opening in software like 3DSmax) ? - why, sometimes, are displayed in the same view the surfacic model as well as the original structure ? My best regards Damien

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(no subject)
by Cédric Govaerts 21 Apr '09

21 Apr '09

Hi there, I want to compute accessible surface area for the backbone, as I want to compare the predicted amide deuteration between two conformations of a protein (I have PDBs for both). I tried with VADAR but the results are puzzling, I suspect they are not correct (the more open structure gets a lower score). Is there a way I can do something like that in Chimera ? In other word I need to compute how exposed to the solvent are the backbone atoms (in fact just the NH) and get a table for every position. Cannot seem to find a simple way to do that with Chimera... Thanks again for your help Cedric Cedric Govaerts, Ph.D. Structure et Fonction des Membranes Biologiques (SFMB) Universite Libre de Bruxelles Boulevard du Triomphe - CP 206/2 B-1050 Bruxelles (Belgium) Tel: +32-2-650.53.77 Fax: +32-2-650.53.82

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Selecting subassemblies
by Brian and Lanie Grech 20 Apr '09

20 Apr '09

Hi everyone In reference to the publication in the March 2005 edition of Structure, titled "Software extension to UCSF Chimera for interactive visualization of large molecular assemblies". Under the subheading "Selecting subassemblies", page 480, it talks about two methods to select part of the outer capsid layer of the model of bluetongue virus and not the inner capsid layers. I am unable to find the documentation explaining how to do this, could someone please direct me to the documentation or explain how to do this. Regards Brian Grech

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spider volumes look incomplete or sliced. Version Linux SUSE 10.2
by booth＠wadsworth.org 20 Apr '09

20 Apr '09

Im having a problem with the latest Chimera version, as well as previous ones for linux2 platform. When loading spider volumes they are imcomplete and sliced. Anyone have any suggestions? A much older version build 2470 from 2007/11/15 runs just fine. Thanks. Tim Booth 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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[Chimera-Users] help with IDLE
by cdlau＠ucsd.edu 20 Apr '09

20 Apr '09

Dear Sir/Miss, I am using the IDLE extensively and I have noticed I cannot paste text or <arrow up> to run previous commands. I was wondering if anyone knew how to change these features or if it is possible. I explored the options>configure IDLE, but haven't found any preference changes that change these problems I am having. Thanks for your help in advance. Best Regards, Christopher

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Straighten a helix
by Francesco Pietra 19 Apr '09

19 Apr '09

I would like to straighten a helix in a complex composition of helices, i.e., at least some of them may vdw interact with each other if moved. Therefore, I plan to let molecular dynamics (MD) changing dihedral angles at the pivot amino acid. I wonder whether chimera might aid through "adjust torsion" or other tool. If not else to provide alternative conformations for input to MD and see if the adjustments converge. Bending of the helix occurs along 5 amino acids, the central one probably the pivot. Thanks francesco pietra

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Re: [Chimera-users] reflection of docking poses with chimera
by Elaine Meng 18 Apr '09

18 Apr '09

On Apr 18, 2009, at 9:43 AM, Antonios Kolocouris wrote: > Hi Elaine, > I have obtained the results of the docking claculations of some > compounds > with a symmetric - by 180 degrees - receptor. To obtain a > consistent set of > structures for further 3D QSAR I need to know how I can reflect a > docking pose by 180 degrees > vertically and horizontally with Chimera. > My kind regards, > Antonios > ---------------------------------------------------------------------- > --------------------- > Antonios Kolocouris, Assistant Professor of Medicinal Chemsitry > Department of Pharmacy, Univ. of Athens, Greece > Hi Antonios, The main issue is figuring out the proper transformation to superimpose one binding site on the other. It will not exactly be a reflection (you will still have the same enantiomers) but a rotation. You would need a recent daily build for what I describe. If you are certain only rotations about the exact horizontal and vertical axis are needed, and you know what the center of rotation should be, use the "turn" command with specified axis and center of rotation to move the ligand model(s). The horizontal axis is x, the vertical axis is y. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> The rest of this message addresses the more general case where the axis of symmetry and thus the proper transformation is not known: -- To find out the transformation, (A) put the two parts containing the two binding sites in different models. This could be done by manually text-editing your PDB file to create two files that can then be read into Chimera. Or, if they are already two different chains, you can use the "split" command to divide the already open model into separate models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> (B) superimpose the two binding sites. It could be done with matchmaker, or match, or manually. Which is best depends on the situation. These methods are discussed and there are links to their manual pages here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (C) find out the relative transformation of the two models using the "measure" command, for example to report the transformation of model #0.2 relative to #0.1: measure rotation #0.1 #0.2 the transformation is sent to the Reply Log (under Favorites menu), both as a matrix and as an axis of rotation and point on the axis, as described in the manual page: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> -- To apply the transformation to the ligands, I would first use the command "reset" (without arguments) to put everything back into their untransformed positions and then either (A) use the "turn" command with specified axis and center of rotation to move the ligand model(s) - or - (B) save the matrix from the Reply Log to a file and then apply it with the "matrixset" command I'm not sure if the "reset" is necessary (some of these transformation issues confuse me), but that's what I would try first. I recommend sending questions to chimera-users(a)cgl.ucsf.edu rather than to me directly, to be certain they will not fall through the cracks. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Superimpose
by Elaine Meng 17 Apr '09

17 Apr '09

Hi Cedric, The "match" command fits whatever atoms you specify: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I should mention that MatchMaker (or "matchmaker" command) generally does pretty well even with low sequence identity because it also uses secondary structure assignments: the score favors aligning helix with helix, strand with strand. However, if you need it, "match" can be used in any situation, including molecules other than proteins and nucleic acids. The tradeoff is that it is more work for the user, since you have to tell it which atoms to use. Discussion of the different ways to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine On Apr 17, 2009, at 8:26 AM, Cédric Govaerts wrote: > Hi Elaine, > > So of course I have a new question: > > Matchmaker will take to proteins, align the sequences and then > align the > structures. > > But what I need to do is to align the structure according to the > pairs of > atoms I have selected. > > For example this could be particularly useful for : > > 1/ Superimpose two structures that are different but have a few common > catalytic residues. They would be two different for Match maker to > find the > correct alignment, however, the user (that's me) would know which > residues > should be used. > > 2/ I tried to superimpose two isoforms of the same proteins using > ions or > ligand as superimposing element. I wanted to see what was the > conformational > change *relative* to the bound metals. > > I believe that creating an alignment for MultiAlign would not work for > either. > > Is there a way I can superimpose two structures after explicitely > choosing > the pairs (minimum) and the Chimera would make a lest-square > regression > based on those ? > > Thanks again > > Cedric >

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making slow movie
by Bala subramanian 16 Apr '09

16 Apr '09

Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded. 1) How can i record a movie with low playback speed. 2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated. 3) Kindly suggest me some better setting to record a movie with high clarity based on your experience. Thanks, Bala

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correction: selecting by element
by Elaine Meng 16 Apr '09

16 Apr '09

Begin forwarded message: >> >> You can use all the end entries in the Select... Chemistry menu also >> in the command line. These symbols are in the element submenu. In >> cases where there is ambiguity, for example H appears both under >> element and under IDATM type, you can disambiguate like >> >> select element.H >> >> It will work to use element.Mg and element.Ca ... it's just more >> typing. > > Hum that does not seem to work oddly. "Select element.Ca" gives me a > "mangled atom specifier" (that why I asked you in the first place). > Same thing for Mg btw (I originally though there was some ambiguity > between > Calcium and carbon-alpha naming). Whoops, my bad. Actually Mg and Ca are not at the top level of "Select... Chemistry... element" but in further submenus. You could use "Md-Ni.Mg" and "Be-Cl.Ca" but I don't think there is a need to use anything longer than Mg and Ca. Ca will not conflict with atom name because the command-line syntax requires @ to indicate atom name. "@ca" are atoms named CA, "@c" are atoms named C, "Ca" are calcium ions/atoms, "C" are carbon atoms. The capitalization is not important for atom names, but it IS important for the things that are also menu entries and should match what is shown in the menu. The potential for ambiguity with element symbols is with the entries under "Select... Chemistry... IDATM type" but in fact H is the only one I can think of that appears in both places. Best, Elaine

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Re: [Chimera-users] making slow movie
by Bala subramanian 16 Apr '09

16 Apr '09

Hi Benoit, Thank you. Actually i was recording the movie with the Record movie option in the MD movie tool where this setting is not there. I will try with movie recorded. Thanks, Bala On Thu, Apr 16, 2009 at 1:26 PM, Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk>wrote: > Hi Bala, > regarding your first point: you can set the number of frames per second in > the movie recorder window. Alternatively, if you encode your movie with a > command line, you can set the number of frames per second with the option > framerate > > Ben > > Bala subramanian wrote: > >> Friends, >> >> I am using MD movie with chimera to see the motion of a single pdb >> containing 25 models. I kept the play back speed at low value, then recorded >> the movie. But the movie comes very fast. I guess there is no related >> functionality between playback speed and the speed with which the movie is >> recorded. >> >> 1) How can i record a movie with low playback speed. >> 2) Is it possible to split the chimera screen in to two halfes or as >> quadrants (like in sybyl) and then load the molecules wherever we want. >> Now why i need it ?. >> I have two pdb files (each consisiting of 25 models). If i can split the >> chimera screen, i would like to load pdb1 left and pdb2 in rigth side using >> MD movie, then record the movie. Any better idea than this to achieve the >> same would be highly appreciated. >> >> 3) Kindly suggest me some better setting to record a movie with high >> clarity based on your experience. >> >> Thanks, >> Bala >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > -- > Benoīt Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber(a)mrc-lmb.cam.ac.uk > >

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How to save fitted map as MRC file.
by 横山武司 15 Apr '09

15 Apr '09

Dear chimera developer I want to save fitted map after using "Tools/Volume Data/Fit in Map" as MRC file. How can I do this? Is there the same kind of function when we save fitted PDB file related to Map. Thank you in advance, Takeshi ------------------------------------------------------------------------------------------------------------------------- Takeshi yokoyama Ph.D. Postdoctoral scientist Wadsworth Center New York State Department of Health USA yokoyama(a)wadsworth.org -------------------------------------------------------------------------------------------------------------------------- _________________________________________________________________ 世の中、仕事は一つじゃない! 自分にピッタリの仕事してますか? http://career.jp.msn.com/article2/genba/default.htm

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Fwd: Copy and Pasting sequences
by Eric Pettersen 15 Apr '09

15 Apr '09

Begin forwarded message: > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: April 14, 2009 2:36:02 PM PDT > To: hsosa(a)aecom.yu.edu > Subject: Re: [Chimera-users] Copy and Pasting sequences > > Oooh, you're right -- that's missing. There's a whole passel of > improvements I need to do for the sequence viewer and now that > you've pointed it out that's certainly one of them. There'll be > some kind of replacement functionality by the next release. In the > interim, a possible workaround is to save the sequence to a file > (using the viewer's File-Save As) and copy from that. Probably the > simplest format (and therefore the easiest to copy from) is FASTA. > > --Eric > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Apr 14, 2009, at 1:22 PM, hsosa(a)aecom.yu.edu wrote: > >> Hi >> >> I noticed that in the latest version of Chimera (1.4) the sequence >> display tool (Model Panel > sequence) is different (nicer looking) >> than >> in previous versions. However, before I was able to copy the >> sequence as >> text and paste it into a text editor (using CTR-C & CTRL-V in >> Windows) >> but that is no longer the case. Is there an easy way to get this >> functionality back. >> >> Thanks >> >> Hernando >> >> >> -- >> ----------------------------------- >> Hernando Sosa >> Dept. of Physiology and Biophysics >> Albert Einstein College of Medicine >> 1300 Morris Park Av. >> Bronx NY 10461 >> phone (718) 430-3456 >> FAX (718) 430-8819 >> email hsosa(a)aecom.yu.edu >> ----------------------------------- >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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coloring with partial charges
by Bala subramanian 15 Apr '09

15 Apr '09

Friends, How to do electrostatic coloring based on partial charges. I have a pdb generated from amber, i would like to assign amber charges and color the surface using assigned charges. Bala

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graphics problems, BIOMT, selecting by element, etc.
by Elaine Meng 15 Apr '09

15 Apr '09

On Apr 15, 2009, at 5:30 AM, Cédric Govaerts wrote: > Hi Elaine, Hi Cedric! I will put responses below, after your individual questions... > > I'm not posting my question to the mailing list because most of it > might be > due to my machine. > I've been encountering some problems running chimeras and I suspect a > graphic card issue(s). > Mostly it's the display that goes bananas, lows the machine ending > (sometimes) in a chimera crash. It's OK -- even if due to the machine, other people have these problems too and might want to see the discussion. > > Here are some of the issues : > > 1/ When I zoom in/out using my mouse wheel sometimes all the > displayed atoms > change from wire to CPK representation. I must explicitely change it > back to > wire to go back. > Normal ? > > 2/ When changing the display I have sometimes some very odd graphic > behavior, including part of the window turing colored or black. I > attach a > couple of screenshots. This started just after typing a display > command. For > a while everything became very slow until I tried to save the image > using > chimera itself which seemed to reset the graphics back to normal. > As you can see on the screenshots, some Photoshop tool windows (PS3 > was > running in the backgournd) appear on the image (although not visible > on > chimera itself) which leads me to think that it's a graphics card > issue or a > graphic card+Photoshop issue. These definitely sound like graphics driver issues. Definitely not normal behavior! Things to try are to update your graphics driver as possible, and/or use the Debug Graphics Driver dialog to selectively disable OpenGL features. One way to show this dialog is to go to Preferences (under Favorites), General category, set "debug OpenGL on startup" to true, quit, and restart Chimera. Documentation of the debug dialog and discussion of graphics driver problems: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html > <http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html> > > 1/ Can I easily build a biomolecule from the PDB file ? > I tried with > i) MultiScale Models but could only get low res surfaces > ii) Unit Cell but got the copies from the SMTRY records of the PDB > file, could not specify the BIOMT > I believe the "sym" command should work but I dunno how to make it > read the > BIOMT matrix in the PDB file. > For building using BIOMT: If you use Multiscale Models, you can force loading of the atomic coordinates for all copies by selecting All chains in the multiscale dialog and then changing the Style to anything other than surfaces. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… > You can also use the "sym" command. If your structure with BIOMT records is model 0, for example, command "sym 0 0": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> > 2/ Is there a way I can select specifically all Mg atoms ? Or - > trickier- all > calcium (Ca) atoms ? commands: select Mg select Ca You can use all the end entries in the Select... Chemistry menu also in the command line. These symbols are in the element submenu. In cases where there is ambiguity, for example H appears both under element and under IDATM type, you can disambiguate like select element.H It will work to use element.Mg and element.Ca ... it's just more typing. > > 3/ When I select with the mouse, I only select one atom at a time. > What > would be the easiest/fastet way to display the residue that the > currently > atom belongs to ? > A/ Can I do it with the command line (does the command line > recognize the manually selected atoms?) ? > B/ I can use the menus and do Actions->Atoms->Backbone->Full and > then Actions->Atoms->Sidechain->Show, but that's a bit cumbersome to > do each > time I wanna see a residue it seems.. If you have some atom or bond in a residue selected, just hit the keyboard up arrow to broaden the selection to the whole residue. That is the same as using the command: select up <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html> You can specify the current selection regardless of how it was created (with mouse, Select menu, etc.) in commands with the word "sel" "selected" or "picked". <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > For example, pick one atom, hit up arrow, use command "display sel" to display the whole residue. Actually if you use "rlabel sel" (show residue label for any selected atoms) you don't even need the up arrow part. > > That's it for now.. brr, thanks ! > > C > You're welcome! Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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interhelical angle
by Shuanghong Huo 14 Apr '09

14 Apr '09

Dear Chimera Developers, My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory. Thanks, Sharon Huo, Ph.D. Associate Prof. of Chemistry & Biochemistry Clark University

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Copy and Pasting sequences
by hsosa＠aecom.yu.edu 14 Apr '09

14 Apr '09

Hi I noticed that in the latest version of Chimera (1.4) the sequence display tool (Model Panel > sequence) is different (nicer looking) than in previous versions. However, before I was able to copy the sequence as text and paste it into a text editor (using CTR-C & CTRL-V in Windows) but that is no longer the case. Is there an easy way to get this functionality back. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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chimera error message
by Michael Zimmermann 10 Apr '09

10 Apr '09

Dear Chimera Staff, I have been trying to learn to use your object model. My goal is to read in an electron density map in CCP4 format downloaded from emdatabank.org and parse out the 3D matrix of electron density values. However, to get started I was trying to just access atomic information in a sample PDB format file (like atomic coordinates). Running through a few of your examples though has proven confusing to me. The following are commands that I have entered into the IDLE. I am using alpha version 1.3 build 2577. >>> import chimera >>> opened = chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb') >>> mol = opened[0] >>> from chimera.colorTable import getColorByName >>> red = getColorByName('red') >>> mol.color = red Traceback (most recent call last): File "<pyshell#42>", line 1, in <module> mol.color = red ValueError: underlying C++ Molecule object is missing Why is there a module missing? How do I find out what module is missing and add it? >>> red.name <built-in method name of _chimera.MaterialColor object at 0x0F1AAF38> >>> red.rgba <built-in method rgba of _chimera.MaterialColor object at 0x0F1AAF38> What if I want the value displayed rather than the object's ID? Is there a get method that has to be invoked? What would the syntax be? >>> ATOMS = mol.atoms Traceback (most recent call last): File "<pyshell#54>", line 1, in <module> ATOMS = mol.atoms ValueError: underlying C++ Molecule object is missing Again, why is a module missing, how do I find out what module is missing, and how do I add it? Thank you, Michael Z

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reading complex-float mrc files
by Benoit Zuber 10 Apr '09

10 Apr '09

Hi, I was wondering if it is possible to read mrc files where the data type is complex float. I get an error when I try to do that, but maybe there is a way around it (other than converting the data to a non complex type). Typically, this would be useful to read fourier transform volumes. Thanks, 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

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deleting arrows
by Bala subramanian 10 Apr '09

10 Apr '09

Dear Chimerians, I created one .bild file and loaded it in chimera. When i use del command the object is not getting deleted. open eg.bild del #0 -> now the arrows that are displayed on the screen is not deleted. Why is it so ? Thanks, Bala

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Renaming chains in "combine" command
by Fajer 10 Apr '09

10 Apr '09

Hi, I am a complete newbie to chimera. I have added a loop sequences to using addaa but the new loop has a different chain designation from the rest of the molecule. "Combine" command preserved the differences in chain id. How can I make the new loop chain to be the same id as the host ? peter

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question
by Tatyana Fedotova 09 Apr '09

09 Apr '09

Dear Mrs/Sir, My name is Tatyana and I am new to Chimera. I hope that you can help me with my question. I have opened pdb file with DNA and protein coordinates. I would like to mutate some residues and base pairs. Do you know how I can introduce them? Thank you, Sincerely, Tanya Tatyana Fedotova, Dpt. of Biochemistry & Molecular Biology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 Cell: 404-386-5950 Office: (315) 464-8734 Fax: (315) 464-8750

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Re: [Chimera-users] chimera difference map
by Eric Pettersen 09 Apr '09

09 Apr '09

On Apr 9, 2009, at 9:23 AM, Negi, Surendra S. wrote: > > Hi Eric, > > I have a quick question related to chimera. Can we use chimera to > calculate the difference map between two EM densities. Hi Surendra, I don't know the answer to this off the top of my head, so I'm cc'ing this to chimera-users, where someone who does know the answer can reply. --Eric

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Modification of b-factor and occupancy
by Tom Goddard 08 Apr '09

08 Apr '09

Tsutomu Matsui wrote: > Hi Tom, > > Is it possible to change b-factor or occupancy of selected atoms, and > then output the coordinates including those changes? > > Tsutomu > Hi Tsutomu, Here are Chimera commands to set bfactor and occupancy of an atom (model #0, residue 13, chain B, atom CA) and write out the PDB: setattr a bfactor 12.3 #0:13.B@CA setattr a occupancy 0.123 #0:13.B@CA write 0 /tmp/test.pdb If you really mean you want change the "selected" atoms use a command like: setattr a bfactor 12.3 sel See the setattr and write documentation for more details. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Tom

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2drms
by Bala subramanian 08 Apr '09

08 Apr '09

Friends, Kindly help me with the following queries. 1) How to output the 2drms created for a md. trajectory using MD movie tool. 2) Is there any way to select a square box of a particular length around the molecule and save the image for publication with the desired resolution. I have seen in the chimera archieve that window size can be adjusted. I am not sure if this is the right way to get my job done. Thanks, Bala

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Enhancement request Povray
by Marhoefer, R (Richard) 08 Apr '09

08 Apr '09

Dear Development Team, I would like to generate raytraced images without any shadows. The shininess however should be retained. I experimented with modifying the povray output and added the "no_shadow" keyword to all objects included in the file. This did the job. Could you please add a "no_shadow" option to the povray options panel? It would be very helpful. Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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