August 2013 - 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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colour by attributes is only colouring one chain of the dimer, how to make the colouring apply to both chains of homodimer
by Anne-Frances Miller 17 Sep '13

17 Sep '13

Dear team Chimers 1- Thank you for GREAT software ! 2- How to make the colouring apply to both chains of homodimer ? I have a homodimer in which features of the active site derive from both monomers so the degree of active site conservation will only show up if I can apply colour by attributes to both monomers (attribute will be conservation) Right now, colour by attributes is only colouring one chain of the dimer, chain A. Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055

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display atom by coordinates
by Bala subramanian 03 Sep '13

03 Sep '13

Friends, I am trying to visualize the md movie of a channel protein. In every frame, i want to display only those ions whose Z coord ranges from -10 to 35 (zcoor of the channel) to make the movie. Is there any simple way ?. Precisely displaying atoms with a condition. Thanks in advance, Bala -- C. Balasubramanian

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Linking two chains in a PDB file
by Maxwell Cherf 03 Sep '13

03 Sep '13

Hi Sir/Madam I have a PDB file of three proteins bound together (in one model). I would like to fuse the N terminus of one protein to the C terminus of another protein by adding a peptide linker between the termini. Is it possible to do this using Chimera? So far, I have built a linker and joined it to one of the termini, but doing that combined the linker and all proteins in the file into one model. Now, I can't connect the free end of the linker to the other terminus because they are part of the same model. Any help would be much appreciated! Best, Gerald Cherf, PhD candidate Cochran Lab Bioengineering Department Stanford University

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help
by rajan sreekanth 30 Aug '13

30 Aug '13

Hi, I had morphed two conformations (open and close) of my protein using 'Morph Conformations' tool. I want know whether we can save the coordinates capturing the intermediate states? Something like an NMR ensemble consisting of the open-intermediate states-close conformations as a single PDB file? Thanks Sreekanth

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Re: [Chimera-users] building a peptide
by Elaine Meng 30 Aug '13

30 Aug '13

Hi Kumud, You would just specify the phi and psi angles for "turn" when building the peptide. You can specify a different phi and psi for each residue if you want, in the peptide building dialog. You do not have to use the values supplied for alpha and beta, you can enter any values, as described in the instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Also, in a peptide structure that already exists, you can change phi and psi for each residue, either ...by rotating the bond interactively (see the Adjust Torsions tab in Build Structure): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> or ...by changing the "phi" and "psi" attribute values in the Selection Inspector (select an amino acid residue in a peptide or protein, click green magnifying glass near bottom right of Chimera window to open the Inspector, Inspect: "Residue" and change the values for "phi angle" and "psi angle") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> However, it is up to you to specify reasonable values. You can check the Ramachandran map by using the "Ramachandran plot" function in the Model Panel (under Favorites in the menu). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/rama…> Although it is possible to build a whole protein with different secondary structures, it would probably have many severe problems (packing etc.) and the basic peptide-building in Chimera is *not* intended for this purpose. You might want to look into using some other program to predict structure instead, or modify an existing protein structure instead of building the whole thing from scratch. There are probably hundreds of programs and dozens of web servers to predict protein structure, but it is beyond the scope of the chimera-users list and my knowledge to discuss the possibilities. 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 Aug 29, 2013, at 11:50 PM, Kumud Agarwal wrote: > Hi, > Thank you for your help. > Is there any way to build a beta sheet in Chimera? How can I introduce > turns in between the strands in beta sheet using the build structure > option in chimera?

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Chimera VTK file reader
by Tom Goddard 29 Aug '13

29 Aug '13

Hi Andrew, I added a VTK file reader -- in tonight's Chimera daily build. It handles vtk structured points files in ascii format like the one you gave me. Your file had many -32768 values which seem to indicate regions where you don't have data and normal data values in a range 0 to 55. This makes the histogram display of data values in Chimera worthless because the data range is 33000 but the meaningful range is 55. Chimera is only able to show the whole range. You might want to use some other value to indicate "no data", like -1 if negative values are not valid. Tom > On Aug 6, 2013, at 10:09 AM, Andrew VanBenschoten wrote: > >> Hi Elaine, >> I hope all is well! Quick question for you: I have a 3D .vtk file (attached) that I want to be able to view in Chimera. This is one of the diffuse scatter maps that we discussed earlier: nearly identical to X-ray diffraction patterns except that the data values are applied to entire voxels as opposed to points. Any suggestions as to what I could try? Thank you so much! >> >> -Andrew >> <out.vtk> > >

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building a peptide
by Kumud Agarwal 28 Aug '13

28 Aug '13

Hi I am very new to Chimera. I am using Chimera version 1.8. I am trying to build a peptide in chimera in beta strand conformation using build structure option but the generated peptide did not show beta strand. Why is it so? Thanks, Kumud Agarwal IIT Bombay India

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Chimera-users August 2013