April 2010 - 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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square of density volume
by 仁田亮 13 May '11

13 May '11

Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

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Re: [Chimera-users] Save session for movie
by Eric Pettersen 18 May '10

18 May '10

Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote: > If at all, I did not understand if a continuous trace of the centroid > (instead of a series of balls) can be obtained in the context of the > protein. That would improve the presentation further. Otherwise, the > series of balls for the centroid, with appropriate choice of radius > and step size, shows the pathway of the ligand through the protein > adequately. Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers. > As a minor point, I was unable to render helices transparent. > Transparency would help to to see the centroid trajectory in between > helices. Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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rmsd between two ligands
by Miriam Gochin 01 May '10

01 May '10

Is there a way in chimera to obtain an RMSD between two structures without matching them, ie. just to know the difference between them? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Volume Subtractions
by Murali Ayaluru 30 Apr '10

30 Apr '10

Dear Chimera users/developers, I have two EM density maps (in mrc format) of a complex with different conformations. I want to subtract one density from another. I am wondering if it is possible in Chimera to subtract the densities? Cheers, Murali

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(no subject)
by Hanzhong Liu 28 Apr '10

28 Apr '10

Dear Chimera Developer: I tried to use Chimera to display MD movie. I tried both CHARMM trajectory and single pdb. They all works. When I put "ksdssp" in the per-frame script, it gave me a warning "name ksdssp is not defined". I used the latest version and the OS is windows 7. But when I ran chimera under windows xp, there is no such problem. I'm wondering if there is a bug of chimera. Thanks!-

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DCD format error 1
by Lilian OLIVIERI 28 Apr '10

28 Apr '10

Hello, I'm having trouble using MD/Ensemble analysis tool. When I try to check a MD trajectory generated by CHARMM (version C33b1), I get a "DCD format error 1" message. Here is the Reply Log: MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. - HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) * THIS FILE IS LANGEVINEEF1.INP. * USAGE, CHARMM <LANGEVINEEF1.INP >LANGEVINEEF1.OUT. * RUNS LANGEVIN DYNAMICS WITH EEF1 IMPLICIT WATER. * DATE: 3/22/10 10:32:48 CREATED BY USER: lolivier /labos/lbgm/lolivier/chimera/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py:121: DeprecationWarning: raising a string exception is deprecated raise "DCD format error 1" Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/DCD/__init__.py", line 61, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/__init__.py", line 71, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/DCD.py", line 35, in __init__ File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ DCD format error 1 DCD format error 1 File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ See reply log for Python traceback. Is there a quick way to fix this problem? Thanks for any reply. -- Lilian Olivieri PhD student INSERM UMR-S 665, DSIMB/LBGM, Faculte des Sciences et Technologies Universite de La Reunion 15 Avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel: +33 262 938 227 (office) Fax: +33 262 938 237 http://lbgm.univ-reunion.fr/ http://www.dsimb.inserm.fr/ **************************************************************************** It has long been an axiom of mine that the little things are infinitely the most important. -- Sir Arthur Conan Doyle, "A Case of Identity" ****************************************************************************

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volume threshold
by Alex Perálvarez Marín 28 Apr '10

28 Apr '10

Hi, there is any command to change the threshold of a density map? I have 100 maps open at the same time, and I want to change the threshold of all of them at the same time. Thanks in advance, best Alex.

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Chimera-users April 2010