- Chimera-users - RBVI Mailing Lists

NMRCLUST
by Austin B. Yongye 04 May '09

04 May '09

Dear chimera users, Does the NMRCLUST algorithm in the Ensemble Cluster tool use Kelley penalty values (Kelley et al. Protein Engineering, 1996, 9(11), 1063-1065) to determine the optimum number of clusters during a clustering procedure? Thanks, Austin-

2 1

Merging models
by Elaine Meng 04 May '09

04 May '09

On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > Hi everybody, > > I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz > ) made of two models. I need to merge this two models into one. How > can I do that? > > Thanks in advance, > > Maziar S. Ardejani > Lab 9, The Orner Lab > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > 21 Nanyang Link > Nanyang Technological University > Singapore 637371 > Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? <http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI> There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols. Please send Chimera questions to chimera-users(a)cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks! 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

5 7

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

2 1

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

2 1

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

2 1

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

1 0

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

2 1

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

1 0

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

3 2

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

2 1

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

3 2

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 -----------------------------------

3 2

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 >.

1 0

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 > >.

2 1

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 >

1 0

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

2 1

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

1 0

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

1 0

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 >> >.

2 2

(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

2 1

[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

3 2

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

1 0

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

2 1

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

1 0

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

1 0