- Chimera-users - RBVI Mailing Lists

Compiling chimera from source code
by cdlau＠ucsd.edu 13 May '09

13 May '09

Dear Madam/Sir, I am currently involved in a project which requires compiling the Chimera source code from scratch. I have been using: http://www.cgl.ucsf.edu/chimera/sourcecode.html for reference, and I understand that surfacing library is not available due to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimera source code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated. Thanks in advance, Chris

2 1

adding pseudo bonds
by Jean Didier Pie Marechal 12 May '09

12 May '09

Dear all, what is the way to add pseubond between metal and chelating atoms? if you could tell me what are the "mouse driven" and "script driven" manner I'll be very pleased.... all the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Diumenge, Maig 10, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 11 > 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. Protonate heteroatoms only (Francesco Pietra) > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Sat, 9 May 2009 23:35:37 +0200 > From: Francesco Pietra <chiendarret(a)gmail.com> > Subject: [Chimera-users] Protonate heteroatoms only > To: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi: > Is there a command in Chimera to protonate (Sybyl-type) the > heteroatoms only (or deprotonate the other elements from a fully > protonated protein)? > thanks > francesco pietra > > > ------------------------------ > > Message: 2 > Date: Sat, 9 May 2009 15:27:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Protonate heteroatoms only > To: Francesco Pietra <chiendarret(a)gmail.com> > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > del HC > > will delete all hydrogens bonded to carbons (their IDATM types are > HC). > --Eric > > Eric Pettersen > USCF Computer Graphics Lab > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 73, Issue 11 > ********************************************* >

3 2

chimera performance
by Bala subramanian 11 May '09

11 May '09

Friends, Is there any way to check the performance of chimera. I have been using chimera without any problems but now it is very slow, in opening even a small dna molecule and manipulating. Is there any way that i can check the root of the problem. Thanks, Bala

2 6

any aid for dock3.5 score?
by Francesco Pietra 11 May '09

11 May '09

Hi: I am considering to use dock3.5 score in DOCK6.2, which makes use of Delphi. Is any aid in chimera for builing the grid? thanks francesco

2 3

Protonate heteroatoms only
by Francesco Pietra 09 May '09

09 May '09

Hi: Is there a command in Chimera to protonate (Sybyl-type) the heteroatoms only (or deprotonate the other elements from a fully protonated protein)? thanks francesco pietra

2 1

changing diameter of the cylinders in bs representation
by Jean Didier Pie Marechal 08 May '09

08 May '09

Dear all, I know how to change the size of the balls using the vdwdefine, but I don't see the command/option to change the diameter of the cylinder in bs representation. Can I do this? best JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Maig 7, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 7 > 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. Re: chimera performance (Greg Couch) > 2. volume filtering (Thomas C. Marlovits) > 3. Re: volume filtering (Tom Goddard) > 4. Re: any aid for dock3.5 score? (Elaine Meng) > 5. Re: chimera performance (Bala subramanian) > 6. Re: chimera performance (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 6 May 2009 12:23:38 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905061215200.1920327(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Wed, 6 May 2009, Bala subramanian wrote: > > > Friends, > > > > Is there any way to check the performance of chimera. I have been > using> chimera without any problems but now it is very slow, in > opening even a > > small dna molecule and manipulating. Is there any way that i can > check the > > root of the problem. > > > > Thanks, > > Bala > > So it was formerly fast on the same computer? This could happen on > a > Linux computer if you updated the kernel and forgot to reinstall > the > graphics driver (from ATI or NVidia, the open source 3D drivers > still need > work, but are improving). Another possibility, on all operatings > sytems, > is that there is a background process that is using a lot of CPU or > memory, so chimera doesn't have the resources it used to. > > If you just want to check the graphics performance, then you can > use the > Benchmark tool in Tool / Utilities to guage the current > performance. And > then you can compare to the reported scores to see if your graphics > performance is reasonable (the Show button in the Benchmark tool > brings up > the web page). > > - Greg > > > ------------------------------ > > Message: 2 > Date: Tue, 5 May 2009 22:34:45 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.ac.at> > Subject: [Chimera-users] volume filtering > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <019F22EC-BFF8-4612-A1B9-BE4DDA9471E3(a)imp.ac.at> > Content-Type: text/plain; charset="us-ascii" > > HI, > > I am trying to look for the various filtering options as descibed > on > the Chimera webpage (guide to volume data display). Indicated are > Gaussian filtering, Fourier filter, Hide dust, etc ... > unfortunately, > I can only find the Gaussian filter option under TOOLS/VOLUME DATA > > but cannot find the others ... can you point me to these other > options, in particular the Fourier filter ? (am using version 1.3 !) > Tx. > -Thomas > > > > -------------------------------------------------------------------- > ----------- > > Thomas C. Marlovits, PhD, M.A.S. > Research Group Leader > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > > >

2 1

volume filtering
by Thomas C. Marlovits 06 May '09

06 May '09

HI, I am trying to look for the various filtering options as descibed on the Chimera webpage (guide to volume data display). Indicated are Gaussian filtering, Fourier filter, Hide dust, etc ... unfortunately, I can only find the Gaussian filter option under TOOLS/VOLUME DATA but cannot find the others ... can you point me to these other options, in particular the Fourier filter ? (am using version 1.3 !) Tx. -Thomas ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

2 1

unable to install on SLES 11
by Rajendra P. OJHA 05 May '09

05 May '09

Dear Users, It gives the segmentation fault and icon disappear. How to rectify the problem. Thanks Ojha

2 1

Fwd: Coulombic Surface Coloring
by Francesco Pietra 04 May '09

04 May '09

---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, May 3, 2009 at 11:01 PM Subject: Re: [Chimera-users] Coulombic Surface Coloring To: Eric Pettersen <pett(a)cgl.ucsf.edu> On Sun, May 3, 2009 at 10:50 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Francesco, > How did you find the page describing Coulombic Surface Coloring, did > you Google it? Yes, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi… Anyway, that tool is only in the daily build, and not in > whatever version you are using. You can get a daily build by going to the > Chimera home page (www.cgl.ucsf.edu/chimera) and following the "Daily > Builds" link. You can install in a location different from your current > version if you like. That way you can use the daily build for the surface > coloring, but use the other version if needed (i.e. if you run into a bug). I'll first see if a program to furnish data for Chimera's Electrostatic Surface Coloring is available. Any suggestion? I forgot that have both apbs and delphi executables as components of an installed docking program. > If your protein consists only of standard residues then I see no > reason for you to use your calculated charges -- the pre-computed Amber > charges should be fine. If there are non-standard residues then it's up to > you if you want to use Define Attribute to add the charges to the structure > or instead rely on Chimera's charge-computation capabilities. My "have a file with calculated charges" was misleading, It was a mol2 file saved with Chimera. thanks francesco > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > On May 3, 2009, at 12:07 PM, Francesco Pietra wrote: > >> 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 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 1

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

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

1 0

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

2 1

(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

2 1

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

2 1

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.

2 1

[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

2 1

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

2 1

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

1 0

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 >

1 0

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

4 5

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

1 0

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 > >

2 1

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

2 1

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 >

1 0

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

2 1

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

1 0

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

2 1

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

1 0

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

2 1

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

2 1

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

2 1

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

2 1

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

2 1

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

2 1

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

2 1

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

3 2

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. --------------------------------------

2 1

python scripts
by christopher lau 07 Apr '09

07 Apr '09

Dear Madam/Sir I am new to Chimera and this forum so I apologize in advance if I my question is inappropriate. I want to start writing python scripts such that I can run the script and the color code, orientation, etc of the molecule opened can be automated. Do you know of any good tutorials that teach what commands are available to use in python for chimera and how to run some basic python scripts in chimera? I have figured out enough to open the Python Shell in Chimera, but that is all. An example python script would be helpful. Thanks everyone, Chris Lau

3 2

chimera help
by Ines COLLINGS 07 Apr '09

07 Apr '09

Dear Madam/Sir, I would like to add the coordinates direction x,y,z in Chimera so that I may know the orientation of the unit cell. Could you let me know how to do this. Thank you very much in advance, Ines Collings

2 1

Re: [Chimera-users] Map Morphing questions
by Thomas Goddard 06 Apr '09

06 Apr '09

Hi Julio, While it is possible to rotate models and use Morph Map at the same time there isn't currently a command to do the morph part. This makes it difficult to record an animation since the morph has to be started by hand from the dialog. The turn command would look like "turn y 3 120" to turn around the y axis in 3 degree steps for 120 steps. Here's the Chimera 1.4 (daily build) "turn" documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html I would like to make a morphmap command so it can be used in animation scripts. Can you explain a bit more your case involving more than 2 maps? Tom Dr .Julio Ortiz wrote: > Hi Tom, > I have been using recently the Morph Map function in Chimera. It is > really helpful! I would like to prepare several movies using this tool. > Three questions: > > 1)Is it possible to combine the morphing with some basic rotations, like > for example around Y axis?. > > 2)I am sure that is doable making some script, but actually..I am so > sorry..I haven't had time to sit down and read carefully how to make > your scripts. > Could you provide me with an initial script to do the rotation of the > morph map which I can start to modify in the future? > > 3) Would it be possible to add more than two maps for the morphing > automatically, and give a sequence of which pairs need to be morphed > instead of make sequential steps? > > Thanks for your help. I hope we can meet again in the near future I > would love to have an update of wht is possible with your wonderful > program. > > Greetings, > Julio >

1 0

Rosetta Academic Training Webinar
by Nir London 06 Apr '09

06 Apr '09

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/

6 13

delay in starting the program
by Eaazhisai Kandiah 03 Apr '09

03 Apr '09

Hi Chimera-Developers, Recently, my work-computer was upgraded from MaC-OS 10.4 to 10.5. I installed the Chimera X-windows version for 10.5. Apparently, while starting the program, it takes almost 2min for the program to get activated. While checking the activity monitor, chimera tries to use 'OSASCRIPT' which together with Chimera, showed as 'not-responding'. I couldn't troubleshoot the reason for this huge delay in start and hence rectify it. Any help would be appreciated. Thank you, 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

2 1

calculating centroid of atoms
by Bala subramanian 02 Apr '09

02 Apr '09

Friends, I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera. Bala

3 2

chimera help
by Terrance Chiang 02 Apr '09

02 Apr '09

Hi, I am trying to show a structural change between two proteins that differ by one amino acid, is this possible with chimera? I was unable to display the transformation I desired, so I looked into other ways to show changes between two overall similar molecules. I found that it is possible to show a change in the surface between two similar molecules, but I am unable to utilize the function because it requires a different file format. I would like to do both... that is, to show the conformational change from one protein to another, as well as show the change in surface from one protein to another, but I keep hitting these road blocks. Any help would be highly appreciated! Thanks, Terrance Chiang

2 1

save reply log via command line?
by Sebastian Kruggel 01 Apr '09

01 Apr '09

dear chimera team / users, i was looking for a way to save the content of the reply log to a text file via command line, because i wanted to embed and process some results given in the reply log in a small cmd/py-script without. thanks in advance, sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel(a)chemie.uni-hamburg.de

2 1

Re: [Chimera-users] write selected command
by Elaine Meng 01 Apr '09

01 Apr '09

Hi Ed, Are there conformational changes in this process, or do chains simply move as rigid bodies? I had thought there were conformational changes within chains, but now looking at your movie again, I'm not sure. If each rigid body is a separate model, you would simply save the different configurations of the entire set as named positions with the command "savepos". Then you can reset to successive named over a specified number of frames with "reset" or smoothly interpolate over multiple saved positions with "fly". There have been recent improvements including addition of "fly" so I'd recommend a recent daily build if it sounds like this approach is doable. The process would then be scripted in a Chimera command file rather than appearing as playback in MD Movie. Once the command file generates the desired movie content, you could put a "movie record" command at the top and "movie stop" and "movie encode" commands at the bottom. example command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples 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

write selected command
by Edward Brignole 01 Apr '09

01 Apr '09

Elaine and co, I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number. Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher. Thank you for your excellent program and support. Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole(a)scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)

3 4

find h bonds
by ROSETTA FORESTIERO 31 Mar '09

31 Mar '09

Hi I have a receptor and more ligands, I want find h-bond between receptor and each ligand using a scripts shell but i have some problem. Can you help me?

2 1

Re: [Chimera-users] Web Access Data
by Elaine Meng 31 Mar '09

31 Mar '09

Hi Thiru, The easy way to tell if a chimerax file is OK is to just try opening it in Chimera with File... Open (file type could be "all (guess type)" or "Chimera web data"). The format is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… > The "name" is the name to use for the local copy of the file from the web, and "loc" is where it is on the web. So "name" is not that important except that it should be the right type (if the file is python, the name should end in .py). As far as I can tell, your chimerax file looks OK. If opening the chimerax file directly in Chimera works OK, but clicking the link on your web page doesn't, your webmaster may need to change a server setting: the MIME type application/x-chimerax should be mapped to the extension .chimerax in the server configuration file. 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 Mar 31, 2009, at 11:47 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > > Thanks for your help. I know it is a delayed response, I did not get > a chance to have a look at it. I am trying to spend some time now on > web access data. > > So, following your instructions, I created a session in chimera and > saved it as a python session, 1A14AgSurface.py > > I was looking at the chimerax file, it had > > <file name="session.py" format="text" loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py > "/> > > it has two .py files, I am little confused about session.py and > 1yey.py > > Here is the 1A14Ag.chimerax file that I have > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="1A14AgSurface.py" format="text" loc="http://www.cs.montana.edu/~tramaraj/Research/1A14AgSurface.py > "/> > </web_files> > </ChimeraPuppet> > > I am not sure if I have the file tag written correctly. > > In my website, I would have something like the following > <a href="1A14Ag.chimerax"> <img src="1A14AgSurface.png"> </a> > > Any help would be greatly appreciated. > > Thank you for your > time and help > > Sincerely > > Thiru R > > > > > > > --- On Tue, 3/3/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Web Access Data > To: thiruvaranganr(a)yahoo.com > Cc: chimera-users(a)cgl.ucsf.edu > Date: Tuesday, March 3, 2009, 10:10 AM > > Hi Thiru, > The session file is python (*.py) ... you cannot just rename it as > *.chimerax. > Instead you would make a chimerax file that gives the names/ > locations of any > files you want to open in Chimera, such as the python session file, > and can > include various Chimera commands. If all you want to do is open the > session, > the chimerax file will be very simple. > > For example, these 6 lines of text are a chimerax file from the > Structure-Function Linkage Database > (SFLD): > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="session.py" format="text" > loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py"/> > </web_files> > </ChimeraPuppet> > > Your web page would link to the chimerax file. Then when the > chimerax file is > opened by Chimera, Chimera will get the session file named inside. > > The page at the SFLD that has this link is > <http://sfld.rbvi.ucsf.edu/cgi-bin/SFLDvm.py?view=family&id=111> > The chimerax file is linked to the large "Active Site" image. > > You can test your chimerax file without using the web just by > opening it in > Chimera. Then if it works, you can link it to a web page, but there > is one more > step: > > If you are using a cgi-bin script to create the chimerax files on > the fly, the > cgi-bin script must specify the Content-type header as application/x- > chimerax. > > If you just have pre-made chimerax files, your webmaster needs to > change the web > server settings so that it sends this information along with the file. > > The chimerax format is described here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… > > > > 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 Mar 2, 2009, at 6:46 PM, Thiruvarangan Ramaraj wrote: > > > Hello All, > > > > I created a session and saved it under .chimerax extension. I have > a link > > to this session on a web page. When I click on this link I wanted > the > > session to open directly using the chimera program. > > > > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… > > > > I tried to follow the instructions given in the above link, still > I am > unsuccessful in figuring it out. > > > > Any suggestions/ideas would be greatly appreciated. > > > > Thank You > > > > Thiru > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

distance measurements
by Jean-Paul Armache 31 Mar '09

31 Mar '09

hello, i would like to ask whether there is a way of automatically measuring the distance from all residues in a chain to residue X in the same chain? best regards, jean-paul armache

2 1

benchmark results page blocked by apache authentication
by Sabuj Pattanayek 30 Mar '09

30 Mar '09

Hi, The Chimera wiki page for benchmarks https://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks has been blocked from being accessed by apache authentication. Thanks, Sabuj

3 2

Fwd: accessible surface area for electron density maps
by David Chenoweth 27 Mar '09

27 Mar '09

Begin forwarded message: > From: David Chenoweth <dchen(a)caltech.edu> > Date: March 27, 2009 8:58:31 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] accessible surface area for electron > density maps > > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods Chimera > is using when it calculates the area (if either)? Is there a way to > calculate the solvent accessible surface area of a molecule with > Chimera or some way to manipulate the current area calculator to > give this value? I also think that depending on the quality of the > electron density map one could get very different results for this > calculation (especially if there is missing electron density or at > different map contour values). If anyone has any advice for the best > way to calculate solvent accessible surface area I would really > appreciate the help. > > Thanks, > Dave Chenoweth > > ********************************************** > David M. Chenoweth > California Institute of Technology > Division of Chemistry and Chemical Engineering > Mail Code: 164-30 > 1200 California Boulevard, 91125 Pasadena > California, USA > > Phone: 626-395-6074 > Email: dchen(a)caltech.edu > ********************************************** > > On Mar 27, 2009, at 8:14 AM, Elaine Meng wrote: > >> Hi Murali, >> If I understand correctly, you want to get the area of a contour >> surface of the density shown using the Volume Viewer tool. If you >> want the total surface area, even of multiple separate blobs, use >> "Measure Volume and Area." If you want to measure the area of >> different blobs individually, use "Measure and Color Blobs." >> >> These can be started from the Tools menu of the Volume Viewer dialog, >> and also from the main Chimera Tools menu (Tools... Volume Data... >> [name of tool]). >> >> For more details on how to use a tool, press the Help button on the >> dialog. That opens the documentation included with your download. >> Our web site also has copies of the documentation: >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol… >>> >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/… >>> >> >> I hope this helps, >> 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 >> >> On Mar 27, 2009, at 7:42 AM, Murali Ayaluru wrote: >> >>> Dear Chimera users, >>> I want to calculate the accessible surface area for an electron >>> density map (mrc format) that I am working on. Can anyone, who >>> knows how to do this, tell me how to do this? >>> Thanks in advance for your reply, >>> Regards, >>> Murali >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > >

3 2

Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi David, As soon as you show a molecular surface, both the total solvent- excluded (molecular surface by Richards definition) and solvent- accessible areas are reported in the Reply Log. It has been like that since before the July 2008 release. The surface that is actually displayed is the solvent-excluded surface. You can adjust parameters that affect the results such as probe radius and atomic radii, but the defaults are reasonable. The area values are also assigned as per-atom and per-residue attributes named areaSES and areaSAS, so you can use Attribute Calculator to get sums over subparts of the surface. For details, see this page and links therein: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces> 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 Mar 27, 2009, at 8:58 AM, David Chenoweth wrote: > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods > Chimera is using when it calculates the area (if either)? Is there > a way to calculate the solvent accessible surface area of a > molecule with Chimera or some way to manipulate the current area > calculator to give this value? I also think that depending on the > quality of the electron density map one could get very different > results for this calculation (especially if there is missing > electron density or at different map contour values). If anyone has > any advice for the best way to calculate solvent accessible surface > area I would really appreciate the help. > > Thanks, > Dave Chenoweth

1 0

Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi Murali, As far as I know, there is no definition of accessible surface area for an electron density map (and thus no way to calculate it in Chimera), only for atomic structures. I'll describe how to get it for atomic structures in my next message, replying to David. 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 On Mar 27, 2009, at 8:18 AM, Murali Ayaluru wrote: > Hi Elaine, > > Thanks for the quick reply. I am aware of calculating the total > surface area of the density maps using Chimera and has been using > it for a long time. Now I am interested in the surface area that a > solvent can access (in otherwords called - (solvent) accessible > surface area). This is a part of the total surface area. Please > mail me if this tool is available in Chimera. > > Regards, > Murali

1 0

accessible surface area for electron density maps
by Murali Ayaluru 27 Mar '09

27 Mar '09

Dear Chimera users, I want to calculate the accessible surface area for an electron density map (mrc format) that I am working on. Can anyone, who knows how to do this, tell me how to do this? Thanks in advance for your reply, Regards, Murali

2 1

Bonds vs. Pseudobonds
by Dipl.-Ing. Thomas Mitterfellner 24 Mar '09

24 Mar '09

Hello again! I have a structure containing Germanium bonded to three oxygens and one methyl group. By default, all of the bonds between Germanium and its valences are considered as pseudobonds and hence drawn as such. In the manual, I read that Chimera uses an algorithm that considers atoms classically bonded if the distance is below the sum of their VDW radii (plus a margin of 0.4 A). However, no matter what I set the radius of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to display a regular bond between Ge and its valences. Can you give me a hint how to set a rule when a normal bond is drawn, or how I can draw one manually? Thank you very much, Thomas

2 1

Using per-frame scripts with color by attribute/bfactor
by Andrew M. Simms 24 Mar '09

24 Mar '09

I am making some MD movies using the multiple-pdb file format. I am using coloring by attribute, in this case overriding the "bfactor" attribute for my own purposes. The nature of my analysis is such that the bfactor can change from frame to frame. I use this command in the per-frame script: rangecolor bfactor,a min white max green However, when I try to make a movie, it appears that the bfactor attribute changes are not reflected in the animation. If I look at generated structures individually they are fine. Is there something special I need to specify in per-frame script? Thanks! --Andrew

2 1

Split colors from Volume Viewer
by Damien Larivière 23 Mar '09

23 Mar '09

Dear Chimera team and users, When opening a map (EMD 1126 for example), the structure is displayed in grey. From the menu Volume and Surface colors, it is then possible to color the structure. I would like to export in the OBJ format the colored structure but this one still appears in grey when I display it in a modeler such as 3DSMax. And effectively, the MTL file created by the exporter only contains one color although the structure displayed in Chimera was multicolored. I look at a tutorial explaining that it is possible to Split map from the menu Volume/color zone. It seemed to me that it is a way to get a multicolored structure in the OBJ format. However, when I want to "split map", a message says "no atom selected". May you tell me how to get a multicolored structure (initially opened from a map) in the .obj format ? All the best Damien

2 1

amd64 installation
by Francesco Pietra 23 Mar '09

23 Mar '09

To deal with very large data files i tried to install chimera-1.3.2577-linux_x86_64.exe in /usr/local/chimera. Mainboard Tyan S2895 dual-opterons; OS Debian amd64 lenny; nvidia chipset 6600, nvidia-glx driver To simplify i made the chimera directory to belong to me as user. The installation from my home succeeded, though chimera did not launch. It appears in part for a moment as if there were no opengl support: francesco@tya64:/usr/local/chimera/bin$ ./chimera X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 626 Current serial number in output stream: 627 I installed libmotif3. Same issue. Once the problem of running chimera is solved, I plan a reinstall in /usr/local/chimera root root. Should I run the installation from my home as superuser? thanks francesco pietra (I run successfully the 32 bit version of chimera on an old Athlon with libmotif3 support)

1 2

addna?
by julien(GWDG) 23 Mar '09

23 Mar '09

Dear all, I would like to know if there is a way in chimera to add nucleic acid to an existing RNA. Something like addna instead of addaa. many thanks 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

Re: [Chimera-users] UCSF Chimera
by Elaine Meng 22 Mar '09

22 Mar '09

On Mar 22, 2009, at 8:36 AM, Tarit Mitra wrote: > Dear Dr. Meng, > I am trying to learn to use the Windows version of Chimera. I would > like to contact a Chimera user in UK. Is it possible to do so? Can > you please help? > With kind regards > Yours sincerely > Tarit Dear Tarit, You could try the e-mail list chimera-users(a)cgl.ucsf.edu (actually I cc'ed it on this message). However, you don't need a live person to help you learn how to use the program. The Chimera download includes several tutorials, some for beginners: choose "Help... Tutorials" from the Chimera menu to see the list. Our Web site has additional tutorials (not just the ones in the Help menu): <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html> Besides the tutorials, there is a complete user's manual (choose Help... User's Guide from the Chimera menu). Just start Chimera and try one of the beginner tutorials, or just experiment, and you will gradually learn! Best, Elaine

1 0

Changing properties by command line
by Dipl.-Ing. Thomas Mitterfellner 19 Mar '09

19 Mar '09

Hello again! I could not find out how to change radii of selected atom via the command line. I had hoped this would work via '@/radius=', which I read in the quick reference, but I turns out that I obviously misunderstood the usage of the hints given there. Is it also possible to change the color and linestyle of coordinative bonds in the command line? Related to this: can the status and color of the molecule silhouette be changed from the command line? Thank you very much! P.S.: Chimera really produces great pictures and I especially like the silhouette effect, which I, up to now, always had to (partially) draw myself with some image editor.

2 1

Chimera does not always recognise atom name in PDB ATOM records
by Christian Schudoma 19 Mar '09

19 Mar '09

Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

3 4

Re: [Chimera-users] Making movies
by Elaine Meng 19 Mar '09

19 Mar '09

> Hi Elaine, > BD simulations is brownian dynamics. Well my file is in a PDB > format, and basically consist of a single complex, with heteroatoms > living from one active site to the other. If you open the file as a > pdb file you will realized the heteroatoms HOH are static. But I > want them to be able to move from the active site of one enzyme to > the other in the complex. > > I was thinking that I can put the word Model, between the complex, > and each heteroatom HOH, so as to make the file seem to have many > pdb files. Hi Neville, Yeah, I eventually realized you meant Brownian dynamics! But what matters for Chimera is the format rather than how the trajectory was generated. To use "MD Movie" to play/record the trajectory, your PDB format options are: (a) put each frame in a separate PDB file The file names must include frame numbers, and files for all intermediate frames must also be present. The files must not contain END records. (b) put all the frames in one PDB file, but bracket each with MODEL and ENDMDL, as is done for NMR ensembles in the Protein Databank, e.g. 1g1p. The MODEL numbers are interpreted as frame numbers and should start with 1 or 0 and increment by 1. Either way, atom names, residue names/numbers need to be the same between frames. ** In general, each frame should have the same number of atoms. However, for "weird" cases where lots of atoms stay in the same position (which if I understand correctly is what you have), we have made a special provision: if the coordinates supplied for a frame represent only a subset of the atoms in the preceding frame, it will be inferred that the remaining atoms are present but have the same coordinates as in the preceding frame. Changes are cumulated in the forward direction and based on all frames, even when frames are skipped during playback. All of the atoms must be in the first frame, of course. In your case, I guess that would include the proteins plus the starting locations of the heteroatoms. You might need to renumber the HOHs to keep their identities across the frames... looks like what you sent gives each position a different residue number. This information as well as how to play the trajectory and record it as a movie are in the MD Movie manual page (choose Help... User's Guide, click Tools tab, click link "MD Movie"). 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

Question about adding a sequence to a previous structural alignment...
by Sergio Garay 18 Mar '09

18 Mar '09

Hi all I've prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. The question is: when I add my target sequence to the profile obtained in the step before, Does this procedure change my previous structural alignment?, or It just aligns the added sequence to my profile. The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension penalties: 12 and 1 respectively. The second problem I have, its not related to chimera, but may be one of you can answer it. My target only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to make my alignment? Any help would be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1

save image error in current daily build
by Ryan Pavlovicz 17 Mar '09

17 Mar '09

Hello, when trying to save an image with the current daily build of Chimera, i am finding that the program closes with the following error: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 10 (X_GLXCopyContext) Serial number of failed request: 0 Current serial number in output stream: 15993 Just wanted to let you know. Thanks, ryan

2 1

Re: [Chimera-users] merge mrc volumes
by Anindito Sen 17 Mar '09

17 Mar '09

Hi Tom Carsten actually just took away my question. Thanks Carsten! It will be really helpful to have such feature ! Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Wed, 18/3/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] merge mrc volumes To: carsten.mim(a)yale.edu Cc: chimera-users(a)cgl.ucsf.edu Date: Wednesday, 18 March, 2009, 5:43 AM Hi Carsten, There's no facility in Chimera to combine (add) maps into a single map though it has been requested by many people and I am anxious to add such a command. Tom carsten.mim(a)yale.edu wrote: > Hi there, > I constructed a model with different .mrc files. Now I want to save the model as > a merged *.mrc file, containing all previous files. > > Thanks > > Carsten > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

merge mrc volumes
by carsten.mim＠yale.edu 17 Mar '09

17 Mar '09

Hi there, I constructed a model with different .mrc files. Now I want to save the model as a merged *.mrc file, containing all previous files. Thanks Carsten

2 1

Changing default element colors
by Dipl.-Ing. Thomas Mitterfellner 17 Mar '09

17 Mar '09

Hello! Can the default element colors be changed easily and if so, how? Thank you, Tom

2 2

Chimera
by taritkumar MITRA 17 Mar '09

17 Mar '09

Dear Sir, I have just installed windows version of Chimera. I am a retired Chemist taken up Molecular Modeling as a hobby. I have some experience of using Spartan and Hyperchem. I would very much like to use the Chimera specially for studies Docking. Are theire any publication or books which will help me in learning to use Chimera. I f so I would like to buy it. Can you please help? With regards Tarit taritmitra(a)hotmail.com

2 1

DICOM maps
by triffo＠rice.edu 17 Mar '09

17 Mar '09

anyone out there know the easiest way to get a DICOM map (typical format for medical CT/MRI data; volume density map; .dcm file extension) into chimera? Is there a translator out there that will reformat DICOM data into a chimera-friendly volume map? thanks, -Jeff

2 1

heme (fe) containing enzyme
by Agus Setiawan 17 Mar '09

17 Mar '09

Hi, I'm a student of Pharmacy and I just learn about chimera.Actually, I want to run a docking using Autodock so I have to minimze the structure of macromolecule first. I choose Chimera to minimize the structure of macromolecule. However, there is an error because the Fe atom doesn't have GAFF"Unable to find GAFF type for #0:500.A@FE"I also have a problem with hydrogen at Histidin residu"no MMTK name for H at standard HIS"How can Isolve this problem?I'll be very thankful for your answers.Best Regards, Agus Lee.

2 1

Re: [Chimera-users] Making movies
by Elaine Meng 17 Mar '09

17 Mar '09

On Mar 16, 2009, at 10:13 PM, yimnai forlemu wrote: > Hello Elaine, > I have a quick question and was wondering whether I can use chimera > to archieve my goals.I have ran a BD simulation and saved > trajectories of my particles. My question is whether it is possible > for me to use chimera to create a movie from the BD simulations > trajectory data.If yes please could you just direct me to the > tutorial that can help me accomplish that goal. > Thanks > Neville Hi Neville, I don't know what "BD simulation" is. Chimera's "MD Movie" tool can read trajectory output from several programs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > If you have one of those formats, or can convert your output to one of those formats (for example, multiple PDB files), MD Movie can show the trajectory. You can control how the molecules look in Chimera as you normally do, then use "File... Record movie" from the MD Movie dialog to create a movie. This tutorial uses the MD Movie tool to do various things, including saving a movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > There are other ways to save a movie (not necessarily using the MD Movie tool). This page has more general information including links to example scripts and other movie-making tutorials: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine P.S. For a reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly. If you send mail to only me and I'm run over by a bus, you will never get an answer!

1 0

Session management suggestions
by Thomas Goddard 16 Mar '09

16 Mar '09

Matt Dougherty sent 4 session file management suggestions. 1) Session description text, browsable. 2) Copying camera positions between sessions. 3) Session version numbers with matching filename extensions. 4) Automated checkpoint session saving. Details below. Tom Matthew Dougherty wrote: > 1) I frequently have to use a lot of session files in combination with a > lot of command files to generate animations. > > One session file might be used with multiple command files. > > I try to pack as much information into the filename as a way to keep it > all organized, but this is becoming cumbersome. > the filenames are becoming cryptic to keep them short; plus I multiple > drafts I need to maintain in case the researcher wants to go back to a > prior visualization. > > It would be good to have a item in the' File' pull-down-menu to handle > summaries or descriptions. > > By activating it, I could type in a paragraph as to what is going on > with the session. > > In a bigger picture, it would be good to be able to start chimera, and > somehow peruse through these descriptions, but not have to load the > session to read the description. > > 2) many times in an animation project I start with a common session file > containing all the data sets in sync, and create multiple derivative > session files to handle different aspects of the animation, usually with > the unused datasets deleted for a particular animation session for > reasons of improving computation speed and loading for a particular > animation clip. > > sometimes I would like to move a set of camera positions created in one > of the daughter session files to another daughter session file. > > Matthew Dougherty wrote: > 1) optional automated versioning. Sometimes I when I am working on an > animation I need to keep the intermediate versions, particularly when I > am less certain about what I am doing and the complexity of the session > goes up. > > check box somewhere that causes saving to automatically prepend "_V22" > before ".py", for version 22 in this example, and _V23 for the next > save, etc. > > 2) optional automated checkpoint saving such that the interval time can > be set. sometimes when working on a complex session it get a crash and > I have not saved it, so I have lost all my work from the previous save, > which could be 1-4 hours.

1 0

Octamer to dimer
by John Lowenstein 16 Mar '09

16 Mar '09

Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks. Sincerely, John Lowenstein

2 1

confocal stack
by Benoit Zuber 16 Mar '09

16 Mar '09

Hello, Is it possible to browse through the planes of more than 1 volume at a time? I have some confocal data and I want to browse along the X axis of the dataset; each volume corresponds to a confocal channel. Cheers, Ben

2 1