September 2011 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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problem in coloring a selected region
by Manish Manish 20 Oct '11

20 Oct '11

Dear Chimera Developer, I want to select a region in protein molecule and then color. I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part. I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915 and Chimera 1.5.3 . Regards Manish

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Ribbon Structures From Gaussian Output
by Michael Lodewyk 30 Sep '11

30 Sep '11

Hello, I'm interested in using Chimera to visualize oligopeptide structures computed with Gaussian09 as ribbon structures... that is I'd like to be able to render an alpha helix backbone as a ribbon and then select specific residues/ligands to be rendered as tube or ball & stick models. While I can save or convert the Gaussian output file to a variety of formats, they do not inherently contain the information necessary for such a rendering of the structure, as one would find in a true .pdb file. So my question is... Is Chimera the correct place to start for creating such representations? If so, can you please point me to any documentation that would assist me in doing so? Thank you, Dr. Michael Lodewyk Tantillo Group, UC Davis

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Using addaa at the N-terminus?
by Tosan Omabegho 30 Sep '11

30 Sep '11

Hi, I read in the manual that addaa can be used at the N-terminus. I'm not having any luck doing this. I've been assigning the amino acid to add at the N-term with a lower number, like: addaa cys,5,alpha :6.a The error message says 'Can only add to last residue'. Is there something I may be doing wrong? Thanks, Tosan

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Chimera for Mac 10.7
by Michael Chou 27 Sep '11

27 Sep '11

Hi Chimera Team, Which version of Chimera do you recommend I download in order to use for Mac 10.7? I downloaded chimera-1.5.3-mac.dmg<http://plato.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac/ch…>. Although it opens, I cannot use any of the features such as any of the actions or presets. Thank you, Michael

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Protein
by sanabaseer＠sbcglobal.net 27 Sep '11

27 Sep '11

Hello, Please help me with managing the chimera program. I have created an image of a protein, but would like to view the active site complex. How can I highlight that in my image? Thank you, Sana Sent from my U.S. Cellular BlackBerry® smartphone

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ribbon display of circular DNA structures
by jens j birktoft 26 Sep '11

26 Sep '11

Hi Everybody How can I display a circular DNA structure with three helices without a break at the places where the ends meet according to the numbering system. In the real structure there is no break in the covalent structure Best Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft New York University, Department of Chemistry. **e-mail: jb160(a)nyu.edu <jens.knold(a)gmail.com> **Phone: 212-749-5057 *

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matrices
by Dougherty, Matthew T 26 Sep '11

26 Sep '11

I was doing something with crystallographic point group matrices. Does Chimera allow for improper rotations and inversions? Or does it rectify them as proper rotations? I would like to go from Model 0.0 1 0 0 0 0 1 0 0 0 0 1 0 TO Model 0.0 -1 0 0 0 0 -1 0 0 0 0 -1 0 Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________

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Chimera-users September 2011