- Chimera-users - RBVI Mailing Lists

Distance between atoms using Python
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Ed, Attached is some Python code for controlling ligand display based on distance between two atoms. Tom Edward Brignole wrote: > > Tom, > > Thanks again for your help with that atom display. Got another > MDtrajectory issue for you. I've got a ligand in each of 10 domains > in the structure and I only want to display the ligands in the frames > that have less than a certain distance between a particular atom in > the ligand and a particular atom in a neighboring domain. > > The distance command won't work for me because all it does is add a > distance to the distance dialog when I need it as a variable in the > script to evaluate with "if distance < 10: display atomspecs" > > Sorry to keep bugging you with these things but I assure you it isn't > without trying for several hours to no avail before finally resorting > to asking. > > Ed > def atom_distance(spec1, spec2): from chimera.specifier import evalSpec atom1 = evalSpec(spec1).atoms()[0] atom2 = evalSpec(spec2).atoms()[0] d = atom1.xformCoord().distance(atom2.xformCoord()) return d from chimera import runCommand if atom_distance('#0:15.B@C4', '#0:7.A@N3') >= 10: runCommand('display #0:SPM') else: runCommand('~display #0:SPM')

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center of mass for multiple models.
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector 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, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > 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 63, Issue 17 > ********************************************* >

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center of mass for multiple models
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector 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, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > 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 63, Issue 17 > ********************************************* >

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Possible image saving bug
by Elaine Meng 17 Jul '08

17 Jul '08

Hi Wally, I also had this tiling problem. We think it may be something about X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not been observed with 10.4/X11. Two workarounds that were successful in my case (I don't know if they will fix all instances of the problem): (A) simply show the Command Line before saving the image. I tried hiding it again after that, but then the problem reoccurred, albeit in a more subtle fashion. (B) save the session, restore it in the aqua version of Chimera (still on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) is easier, but I didn't discover that one until this morning, after receiving your mail. I hope these solutions are general! Sorry about the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Possible image saving bug
by Walter Novak 17 Jul '08

17 Jul '08

Hi All, I submitted a bug report on this, but the behavior is both odd and reproducible for me. Using the latest production release and trying to save an image using supersampling, the image is not stitched back together appropriately. It is odd, because it always happens for a certain session file I have. It doesn't seem to happen if I open a new molecule and make a picture. I can provide the session file if needed. First image is using 3x3 and second is 6x6. Also, when using pov-ray, the balls are completely devoid of shininess, regardless of my shininess settings (I set it to 128). That is the last image. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Coloring a binding site
by Tom Goddard 16 Jul '08

16 Jul '08

Hi Andy, To color a binding site I would select the ligand (DNA in your case) then select all the nearby atoms using Select / Zone..., then use Actions / Color to color those atoms. Tom Anindito Sen wrote: > Another question - I need to color a portion of the crystal structure > differently (ribbon diagram) in order to indicate the binding sites of > the DNA with the protein molecule and how do I do that. > > Thanks and Best Wishes > Andy

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possible bug
by Ben Keshet 16 Jul '08

16 Jul '08

Hi, when I un-select atoms, I had some weird long lines crossing my structures across (picture attached). I restarted the program how ever the same exact thing happened again. The two files that were opened worked perfectly in the past and before I un-selected the atom (ctrl+left click in the "air"). Other wise - great software. Thank you. Ben

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Re: [Chimera-users] History feature for command line between sessions
by Eric Pettersen 15 Jul '08

15 Jul '08

> On Apr 17, 2008, at 8:52 AM, Boaz Shaanan wrote: > > > The history of commands in the command line mode is retained > > within a session and is very convenient but I was wondering whether > > there is a feature that will allow you to recall commands from > > previous sessions (such as in O for example - it generates an .o- > > history file which is being constantly updated and is very > > convenient). If not, is it possible to request the addition of such > > a feature ? There are many ways to implement this of course and I'm > > sure you'll find the best way, if it's not already there lurking in > > Chimera. > > Hi Boaz, > Good idea -- and shouldn't be too hard to implement. I was thinking > of remembering the last 100 commands. Will that be enough you think? > > --Eric This is implemented now. It should show up in the next daily build that works. Only remembers 60 by default, but that number is changeable in Preferences. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Can't type in Chimera
by Thomas Goddard 15 Jul '08

15 Jul '08

Hi Andy, I don't know how Chimera could get in a state where it will not accept any typed input. Do you recall the last thing you did in Chimera before it stopped accepting key input? If I were stuck in this situation and could not type a file name to save the Chimera session I would create an empty file with the session file name I wanted using a text editor. Then choose that file with the mouse in the Chimera session saving dialog. Desperate measures. If you can reproduce the problem please tell me how and I will fix Chimera. Tom Anindito Sen wrote: > HI Tom > > I have installed the latest version of Chimera on my LINUX box Fedora > Core 6.0. I faced a strange problem- while carrying out a docking of a > crystal structure in a density map I was using the command line for the > differnt movements and controls. After some time I am unable to type > anything on the command line. Infact I am even unable to save the > session as I cannot type the "NAME" of the session. I checked my keyboad > and typed on the terminal and on text editiors and it worked normally. > > Waiting for your response. > > Best Wishes > Andy > > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

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Re: [Chimera-users] reg. ribbon reprsentation
by Elaine Meng 15 Jul '08

15 Jul '08

>> >> Greetings. I have already posted a similar question on the forum >> previously and hence i am writing to your email. My problem is when >> i open a protein pdb, i get wonderful ribbon representation when i >> opt for it. But when i give a protein pdb with only a CA atoms/ >> CA,C,N atoms, i dnt get the ribbon representation. I understand >> that ribbon is constructed by considering CA,C,N,O and OXT atoms. >> What i did was that i simply removed O and OXT atoms by going >> through Tools--> Depiction --> Ribbon style Editor. It may be a >> wrong idea to do that. But i would appreciate if you could write me >> some way to draw the ribbon for protein having only CA or CA,C,N >> atoms IF POSSIBLE. >> >> Regards, >> Bala >> Hi Bala, If you have N-CA-C atoms, it actually works pretty well if you open Ribbon Style Editor, go to the "Residue Class" tab, choose "amino acid" but then change the "Orientation atom" to C instead of O, and Apply. (You still need to show ribbon if you didn't already do that.) You can save and name the new residue class for re-use in some later Chimera session if you want. The resulting ribbon looks the same to me as the standard ribbon made from N,CA,C,O (I tested this by writing a PDB of only the N,CA,C atoms from a complete structure, reading it back in, and experimenting with Ribbon Style Editor). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon… If you have CA atoms only, then there is no way to figure out the plane of the ribbon - it does not work to set both the "Guide atom" and "Orientation atom" to CA. Unfortunately this prevents you from displaying "licorice" ribbons even though they don't use an orientation plane. My only solution in this case is to use some program to build the additional atoms from the CA trace, for example this web server: http://www.ebi.ac.uk/Tools/maxsprout/index.html 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

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Re: [Chimera-users] email address
by Khanei Mkumeni 14 Jul '08

14 Jul '08

khmlukundo(a)gmail.com

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SpaceNavigator with Linux
by D. Greening 14 Jul '08

14 Jul '08

Hi, I just downloaded Chimera 1.2540 and was pleased to see that the SpaceNavigator 3-D mouse is now supported for Windows and Mac. Will those of us who use Linux be able to use our SpaceNavigators with Chimera any time soon? Thanks. D. Greening Memorial University of Newfoundland

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drawing molecules
by Kathleen.Zocher＠ernaehrung.uni-giessen.de 14 Jul '08

14 Jul '08

Dear Sir or Madam, I`ve just one question concerning some special tools of Chimera. Is it possible to draw small molecules (ligands) within chimera? I can not find some information for this problem in the manual. For further docking experiments I just need a 3D-structure which is minimized (in a mol2 file). Many thanks in advance! Sincerely yours Kathleen Zocher ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Question about bond length modification
by Benjamin G.S. Horsman 14 Jul '08

14 Jul '08

Hello, I have what appears to be simple problem but is I can't find the solution in previous mailing list queries. My problem is that I am unable to modify the lengths of any bonds in a PDB molecule. I am rather frustrated with myself over such a stupid problem, having tried dozens of times over dozens molecules to get it right but to no avail. Any possible solutions from the community? I am using MacpyMol to generate PDB structures and Chimera v1 build 1470. Thanks for any help, Ben

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Re: [Chimera-users] [Chimera-announce] Chimera production release
by Elaine Meng 13 Jul '08

13 Jul '08

Hello Yao, Don't worry, the new versions still include the ability to fit map in map. It is simply that two tools were combined into a new tool with a slightly different name. Changes in this production release relative to the previous one include: "Fit Model in Map" and "Fit Map in Map" (Volume Data) — * merged into new "Fit in Map" tool * can update fit values continuously * can simulate map from atomic coordinates, report map-map correlation current documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ fitmaps/fitmaps.html Best, 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 Jul 12, 2008, at 11:49 PM, Yao Cong wrote: > Hello Chimera developer, > > Appreciate your great efforts to make Chimera an perfect tool for > Cryo-EM study. > > I and many of my colleges notice that in your latest versions, you > omit the "fit map into map" module, which is very convenient in > many cases. Is there a specific reason for that? And we all > consider it will be very helpful if you could add this function > back in your next version, maybe daily release? Otherwise, we still > keep the old version to have that function and meanwhile install > your newer version to enjoy the newer functions. > > Thanks, > Yao > ----------------------- > Yao Cong, Ph.D. >

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Creating abridged multimer
by Francesco Pietra 12 Jul '08

12 Jul '08

I am posting again after having once again subscribed In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route? (1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit? (2) Build the unabridged multimer and proceed to simplify each subunit the same way? Thanks francesco pietra

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distance measurements on surfaces
by Daniel Hautzinger 10 Jul '08

10 Jul '08

Dear all, from the Volume Visualization Tour, I discovered the topography command that now allows me to dsiplay atomic force microscopy data (basically bitmap images with grey scales representing height). In that way I got some very nice images. I also found out how to scale the voxel size, so the scale of the structures should be correct. To test this, and to be able to add some length markers, I wanted to measure distances on the surface generated by the topography command. But while that seems possible for volume data (by setting markers), I had no success with the surface representation of my data nor the original image (which is handled as kind of a volume, but a single slice) when it came to setting markers or measuring distances in another way. Did I miss anything, or is that just not possible? I am using build number 2509, because of the topography feature. Setting markers is described as working by setting the marker in the first maximum in the line of sight at the click position. For surfaces, you could just take the position of the visible pixel clicked. Or maybe it is possible to convert surfaces to volumes? Thank you for your help Daniel Hautzinger

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changing selection color
by Michael DiMattia 10 Jul '08

10 Jul '08

Hi all, I have a quick question regarding a figure I am trying to make. I have a multi-chain protein loaded with each subunit surface-rendered individually. We wanted to find a way to highlight the outline of one of the subunits in the 3d surface rendering and selecting the surface of the chain works really well for this in Chimera. The familiar green outline highlights the subunit well, even though I realize this is probably not the primary purpose for such highlighting. I imagine it is just to let the user know what is selected. But if i were to use the selection highlighting to show such an outline in a figure, i was wondering if it is possible to change the color of the selection outline from green to any other color or if it is possible to change the width of the outline. I realize it's a long shot, but thought I'd ask anyway in case anyone has tried this before. Many thanks Mike DiMattia

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Chimera production release
by Elaine Meng 10 Jul '08

10 Jul '08

Hi everybody, A new production release, version 1.2540, is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html For the time-challenged, here are just a few of the reasons you may want to use the new version: 1) new fetch types: - comparative models from ModBase - protein pocket data from CASTp database - small molecule structures from Pub3D - small molecule structures built from SMILES strings 2) surface improvements: - increased reliability - surface areas automatically calculated - Actions menu, other tools work on more types of surfaces 3) appearance: - default lighting changed to improve POV-Ray results - larger default scale - helix ribbon insides can be colored separately - 2D labels can include Greek letters and other symbols 4) new tools: Axes, EnsembleCluster, Solvate, Structure Diagram 5) new commands: export, mclip, molmap, perframe, ribinsidecolor, shape, solvate, topography, vop See the release notes for details. The production release includes versions for Windows, Mac/X11, Linux, SGI IRIX, and HP Tru64. The Mac Aqua version has been improved significantly, but for now remains a snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Enjoy! The Chimera Team

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Multiscale models and surface coloring
by David Sept 09 Jul '08

09 Jul '08

I need to create a series of images of large protein complexes, and since it is tedious to do this through the menus, I am trying to script this for Chimera. I want to create low-res, EM looking surfaces and color the individual protein chains different colors. So far, I can read in multiple structures and create the surfaces, but I can't figure out how to change the coloring. Here's what I have: ---- test.py ------- from chimera import openModels m = openModels.open('model-1.pdb')[0] import MultiScale d = MultiScale.show_multiscale_model_dialog() d.make_multimers([m]) chimera.viewer.viewAll() ---- test.py ------- The above python script work and makes very nice blobs. I can color the entire structure (say red) by adding something like: d.select_all_chains_cb() d.change_color_cb((1, 0, 0, 1)) but I can't figure out how to select individual chains and color them (not sure how to use select_chains). This also gets more complicated when I load in two structures at the same time and they have common chain letters. Since I found a way to get this (almost) working in python, I've been sticking with it, but if this can easily be done directly using a chimera command file, I'm happy to do that. Any help is appreciated. Thanks, Dave ---------------------------------------------------- David Sept, Ph.D. Associate Professor Biomedical Engineering and Center for Computational Biology Washington University, Campus Box 1097, St. Louis, MO 63130 Phone: (314) 935-8837 Fax: (314) 935-7448 dsept(a)biomed.wustl.edu http://habanero.ibme.wustl.edu

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Coloring different set of marker with different radius
by Bui Khanh Huy 08 Jul '08

08 Jul '08

Hi, I tried to color my EM electron density and thought that if I can color different maker sets with different radii, that would make thing much easierMy idea is to color one set using radius a, then select another set, color with radius b. But then the color from the first set disappeared. . Is there any way to do that? Best regards, Huy

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Mac Chimera in-window menu bars
by Thomas Goddard 07 Jul '08

07 Jul '08

Hi Kevin, The Chimera Aqua version has a menu bar at the top of the screen as normal Mac applications do and also at the top of the graphics window. I agree there should be a preference setting to eliminate the in-window menu bar. Here's the reason for this weirdness. There are 13 Chimera dialogs that have their own menu bars and menus. Use of these involves switching between actions in the main window and the dialog repeatedly. With menus for the active window only shown at the top of the screen this interaction becomes very tedious. For this reason I added menu bars within each Chimera window that has its own set of menus. Those in-window menus don't work very well. If you post one menu then put the pointer over an adjacent menu it will not pop up. An even worse atrocity in Aqua Chimera is that it implements "focus follows mouse". As the pointer is moved over the various Chimera windows the one underneath becomes active. This again was added because common Chimera usage involves switching frequently between windows and the normal Mac "click to focus" behavior is inconvenient for this. We would like instead to use "click through" where the first mouse click on a window both activates that window and presses the button or activates the entry field that was clicked on. I have not been able to do this in Aqua Tk, the windowing toolkit we use. The problem we're facing is that the Chimera user interface with its many windows and frequent switching between windows is poorly suited to the Mac GUI conventions. The in-window menus and focus-follows-mouse mode are a first stab at a compromise solution -- still much to be desired. Tom Kevin Walzer wrote: The latest build of Chimera from 7/3/08 on OS X/Aqua (10.5.4) includes menubars at the top of the screen (the standard OS X behavior) *and* on the main toplevel window itself, as on Windows and X11. This behavior is simply weird--two menus? It can only b e regarded as a bug, not a feature. What purpose does it serve? The correct Mac behavior can be restored by commenting out lines 1470-1476 of tkgui.py. If some of your Mac users are requesting this kind of behavior in menubars, at the very least the non- standard window-based menubar should be a preferences item that can be toggled off.

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Tile Structure default view
by Eduardo Sanz Garcia 07 Jul '08

07 Jul '08

I would like to request an extra feature for chimera, if it is not there already. I normally open multiple structures in chimera and then I use the "Tile Structure" button to visualize them in an array. This is nice, for example, to visualize the evolution of a cryo-EM 3D reconstruction. I would like that chimera could open multiple structures in an array view by default. Could a "Default view" button be added to the Tile Structure window, so that the "Border scale" value setting is saved and then the next time I open several structures they would be displayed in array view? Thank you very much.

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renumbering pdb
by bustik＠gmx.net 05 Jul '08

05 Jul '08

dear chimera-users, i am just starting to use chimera, so this will be a really simple question to you (although i didn't find anything about this in the manual...): is there a simple command to change residue numbers in a pdb file (i built up a homology model and want to elevate all residue numbers in the model the same amount)? thanks in advance sebastian -- Sebastian Kruggel Eppendorfer Weg 17d D 20259 Hamburg fon: +49 (0)40 4192 9579 mobil: +49 (0)151 1789 2232 e-mail: bustik(a)gmx.net

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graphics performance: amira v. chimera
by Matthew Dougherty 02 Jul '08

02 Jul '08

I loaded a MRC file, isosurfaced it, gave it a transparency around 0.48, and generated a vrml in chimera. I loaded the vrml into amira. initial comparison: I reloaded the vrml into chimera, I turned off the fog on chimera, moving the object around the refresh rate seems to be around 8 fps. On amira it seems to be around 24fps. results: The graphics on Chimera seems to be better during the rotation of transparent objects: full rotation in chimera is flawless, full rotation in amira results in flipping of the object (vertices in back quantum-ly jump to the front, front vertices go to back, looks like a z buffer error) periodically at 180 degrees, making it useless for many camera positions. Any comments or suggestions?

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