- Chimera-users - RBVI Mailing Lists

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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