- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids
by Tom Goddard 12 Dec '08

12 Dec '08

Hi David, By probability level do you mean occupancy? You could change the script to show only atoms with > 50% occupancy by changing: for a in atoms: perMol.setdefault(a.molecule, []).append(a) to for a in atoms: if a.occupancy > 0.5: perMol.setdefault(a.molecule, []).append(a) Tom David Chenoweth wrote: > Hi Tom, > > Thanks for the script and all the help. The script works great, but I > was just wondering if there is a way to set a probability level (50%)? > > Thanks again, > Dave > > On Dec 12, 2008, at 9:58 AM, Tom Goddard wrote: > >> The script for drawing aniosotropic b-factor ellipsoids makes uses >> 1280 triangles per ellipsoid surface which slows down your graphics >> for cases with more than 1000 ellipsoids. You can reduce the >> "subdivision_levels = 3" in the script to "subdivision_levels = 1" to >> use just 80 triangles, or to a value of 2 for 320 triangles. The >> number of triangles controls how smooth the ellipsoid looks (T = 20 * >> 4^S, S = subdivision_levels). >> >> Tom >> >> >> Eric Pettersen wrote: >>> On Dec 10, 2008, at 3:41 PM, David Chenoweth wrote: >>> >>>> Dear Chimera team, >>>> >>>> It looks like preserving PDB ANISOU in Chimera is now a solved >>>> problem and I was just wondering if the ability to display >>>> anisotropic temperature factor ellipsoids would be added soon. Our >>>> small molecule lab and molecular observatory at Caltech is starting >>>> to use Chimera and I think small molecule crystallography labs in >>>> general would use Chimera more if this feature were available. I do >>>> have to admit that I am interested in this feature for selfish >>>> reasons. I am using Chimera for several publications and for the >>>> graphics in my thesis which, has to be finished in the next couple >>>> of weeks, and I would really like to use this feature. >>> >>> Hi Dave, >>> Yes, reading/preserving the ANISOU info lays the groundwork for >>> eventually showing anisotropic ellipsoids. There's still a lot of >>> work to go before showing the ellipsoids becomes a usable feature of >>> Chimera. It might make it into our next release (middle of next >>> year) and it might not. As a stopgap, I've attached a script that >>> will show ellipsoids for any currently selected atoms. You can run >>> it by simply using File->Open or the "open" command. The first two >>> lines of the script control the size and color of the ellipsoids, so >>> change them if you like. The script leverages some code that Tom >>> Goddard wrote for showing principal axes of inertia as an ellipsoid. >>> Good luck with the thesis! >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> http://www.cgl.ucsf.edu >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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(Thermal ellipsoids) anisotropic temperature factor ellipsoids
by David Chenoweth 12 Dec '08

12 Dec '08

Dear Chimera team, It looks like preserving PDB ANISOU in Chimera is now a solved problem and I was just wondering if the ability to display anisotropic temperature factor ellipsoids would be added soon. Our small molecule lab and molecular observatory at Caltech is starting to use Chimera and I think small molecule crystallography labs in general would use Chimera more if this feature were available. I do have to admit that I am interested in this feature for selfish reasons. I am using Chimera for several publications and for the graphics in my thesis which, has to be finished in the next couple of weeks, and I would really like to use this feature. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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drawing a symmetry axis
by Philip Wurm 12 Dec '08

12 Dec '08

Hi, i have a protein dimer and i would like to show the symmetry axis. I found a script in this mailing list: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html which works quite nice. But i would like to have a nicer representation of my symmetry axis, not this two slabs. Just a line or thin rod would be nice. Does anyone know how to do this? Thanks, Philip

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Re: [Chimera-users] problems before even getting to the plate...
by Jon Kenniston 12 Dec '08

12 Dec '08

Thanks guys, I have it working now. The problem was with the specific type of PDB I was using. Incorrect info from a labmate... Jon On Dec 12, 2008, at 12:27 PM, Tom Goddard wrote: > I also tried 1.3 on a PPC Mac 10.4.11 desktop in the lab and it > correctly displayed PDB files. > > Tom > > Elaine Meng wrote: >> Hi Jon, >> I just tried Chimera Mac/X11 version 1.3 build 2577 on a Mac >> laptop, OS 10.4.11 along with X11 1.1.3, and was able to open >> various PDB files (local and fetched from the RCSB) and manipulate >> them. Must be something else in the details of your system - >> perhaps it will be evident from the information that comes with >> the bug report. >> Best, >> Elaine >> >> On Dec 11, 2008, at 11:46 AM, Greg Couch wrote: >> >>> On Wed, 10 Dec 2008, Jon Kenniston wrote: >>> >>>> Howdy, >>>> >>>> Trying to run latest Chimera release version 1.3.2577 on my OSX >>>> 10.4.11 with X11 version 1.1.3 and while the chimera program >>>> opens, I >>>> cannot open a PDB (or at least I can't see the opened PDB - no >>>> error >>>> message, and bottom left of chimera screen states "Opened XXX.pdb" >>>> for about a minute until it goes to blank). Should I try >>>> installing >>>> an older version of chimera? Any help would be much appreciated. >>>> >>>> Thanks, >>>> >>>> Jon >>>> >>> Please use the Help / Report a Bug dialog to get this bug into our >>> bug >>> database. It will tell which model Mac you have and what >>> graphics card it >>> has, so we can try to reproduce the bug locally on similar hardware. >>> >>> The next step would be to try the 1.3.2577 Aqua version of >>> chimera. And >>> if that doesn't work, then try an older version. If one or none >>> of those >>> work is important to know too. All of the versions can coexist >>> on your >>> Mac if you give each version of chimera a different name. >>> >>> Greg Couch

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Worm color gradient
by Markus Voehler 11 Dec '08

11 Dec '08

The worm tool has many wonderful options to adjust the ribbon size according to the b-factor or occupancy, including the options of abruptly changing the radius for each residue or a smooth change. It also allows to change the colors varying on the values used. I can not find an option to display smooth transitions for the colors that would correspond to the smooth transition of the radius. All I see is the color changing abruptly for each residue. Is a smooth color transition available? Sincerely, Markus

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suggestions
by Matthew Dougherty 10 Dec '08

10 Dec '08

1) session name somewhere on the viewer, perhaps next to "UCSf Chimera" at the top. 2) make the session name accessible as a variable name for text labels. So the first 10 frames of a movie can embed the session name. 3) ability to create movie file names using the session name variable; so that movie filenames can be automatically derived. 4) ability to set different directory defaults (e.g., data working directory, directory containing session files, directory containing movies)

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Re: [Chimera-users] biomt transform
by Elaine Meng 10 Dec '08

10 Dec '08

On Dec 10, 2008, at 10:39 AM, Connie Oshiro wrote: > > I would like to generate the "biologically relevant" form of a > protein, based upon the pdb BIOMT record and am having some > problems. I'm running chimera alpha version 1 build 2566 2008/10/16 > on win32 > > I tried 2 different methods, with different results: > > using pdb file 1LT8 > on the command line: > select #0 > sym #0 #0 > > GUI: > Tools -> Higher Order Structure -> Multiscale Models...Select chains > "All"....Under Multimer: Biological oligomer, click on "Make Models" > > In the first case, coordinates were displayed. I'm guessing they > are correct, or at least the correct number of structures were > generated. > > In the second caes, I got a kind of a surface in the same area in > space, but not the "usual" ms (msms) surface, with no coordinates. > > Questions: > - Are the commands I used on the command line correct? > - If I want to use the GUI, what am I doing wrong? > > thanks, connie Hi Connie, You did everything right. Both "sym" and Multiscale Models can use BIOMT to generate the corresponding multimer. The "select #0" command is not necessary, but it doesn't cause a problem. By default, Multiscale Models makes the extra copies as low-res surfaces for efficiency since you might be generating a colossal multimer (with zillions of atoms). To force loading full atomic coordinates of all of the copies, use the Multiscale Models dialog to select "All" chains, then change the style (representation) to anything other than surface. Once the chains are selected, you can use either the Multiscale Models dialog or the Actions menu to hide the surface and show ribbons or some atomic representation. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/multisc… > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#secondary > Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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] Generated density maps
by Tom Goddard 10 Dec '08

10 Dec '08

Hi Maya, Chimera does not write CCP4 format. I am surprised that Coot does not read the MRC map. Does it give an error message? Have you tried changing the file suffix to whatever Coot expects (.map?). The differences between MRC and CCP4 format are very small and usually do not prevent these file types being read interchangably. Tom maya shcushan wrote: > Dear Tom, > > Indeed, the program Coot cannot open the .mrc map that Chimera produced. > Since Chimera can deal with both .mrc and .ccp4, I guess you have some > function inside Chimera that can convert the formats. Still, chimera allows > to doesn't allow to save in .ccp4 format. > > The point is I need it in the .ccp4 format. Can something implanted in > Chimera do that for me? > > Thanks, > Best, > Maya > > -----Original Message----- > From: Tom Goddard [mailto:goddard@cgl.ucsf.edu] > Sent: Wednesday, December 10, 2008 7:45 PM > To: maya shcushan > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Generated density maps > > Hi Maya, > > The MRC format is almost identical to the CCP4 map format. Most > software that expects a CCP4 map will have no trouble reading an MRC > map. The main difference is in how they specify the positioning of the > map. The MRC map written by Chimera may not align with the PDB if > opened in a program that is expecting a CCP4 map. (I suspect it will > align in most other programs.) > > Tom > > > maya shcushan wrote: > >> Hello, >> >> I generated a density map of 8A resolution from a PDB file. I would >> like to save the map in CCP4 format, but Chimera only allows me to >> save it in .mrc, .nc, .cmap and .brix format. IS there any way to >> save it in .ccp4 format, supported by chimer? >> >> Thanks, >> >> Best, >> >> Maya Shuchsan, Tel-Aviv University >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > >

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using EMAN/AIRS/SSEHunter
by Peter Hildebrand 10 Dec '08

10 Dec '08

Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: <function command at 0x89f67d4> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter

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Combining volumes in the new Chimera version
by Martin Kampmann 10 Dec '08

10 Dec '08

Hello, I just downloaded the new Chimera version and tried to combine different models (density maps) into one volume, using the new 'combine' function, (e.g. combine #1 #2), but it returned an error message. Is it only possible to combine atomic structures (such as PDB files), or is there a way to combine volumes/density? Thanks a lot! Martin P.S.: Thank you so much for developing Chimera! I enjoy working with this program a lot! . . . . . . . . . Martin Kampmann The Rockefeller University 1230 York Avenue New York, New York 10021 USA phone: ++1 212 327 8101 fax: ++1 212 327 7880 e-mail: Martin.Kampmann(a)rockefeller.edu

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