- Chimera-users - RBVI Mailing Lists

possibilities to save parts of models (selection)?
by Sebastian Kruggel 17 Dec '08

17 Dec '08

Hi all, is there a simple way to save incomplete models (eg the current selection)? The write command seems to work only with complete models and not with atomic specifications and the split command does only give me the possibility to split complete chains. Probabaly I just don't see something *very* easy... Thanks for help! Sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 D 20146 Hamburg Tel +49(0) 40 42838 3626

2 1

Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids
by Eric Pettersen 16 Dec '08

16 Dec '08

On Dec 11, 2008, at 3:43 PM, David Chenoweth wrote: > Hi Eric, > Thank you very much for the ellipsoid script! I really appreciate > your help and I think this will do the trick for now. I have been > learning some python on my own and I was wondering if you have some > good beginner examples of scripts for making geometrical shapes, > changing size and color, orientation, etc. that work in chimera. Hi David, You can show cones, arrows, boxes, and a variety of simple geometric shapes by opening a BILD format file in Chimera: BILD format. It may be a little awkward having a script write a temporary file, so instead you can use a StringIO object, as described here: [Chimera-users] BILD object question You can also use the 'shape' command to draw spheres, cylinders, and icosahedrons. You can run any Chimera command from Python by using Chimera's 'runCommand' function, e.g.: from chimera import runCommand runCommand("shape sphere center ligand color dodger blue radius 25") Feel free to ask more questions! --Eric

1 0

Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids
by Tom Goddard 16 Dec '08

16 Dec '08

Hi David, Ok I see now, it's a matter of choosing the size of each ellipsoid to have a 50% chance of finding the atom in that volume. This shouldn't be too hard but I'll let Eric tackle it if he has time. Tom David Chenoweth wrote: > Hi Tom, > > Here is the description of the thermal ellipsoids and option to change > the probability lavel from the Raster3D page. > > -prob Plevel > By default, isosurfaces are drawn to enclose the 50% probability > level in the probability density function described by the Uij values > in the ANISOU record. The -prob option allows you to select a > different probability level instead. If 0<Plevel<1 this value is > interpreted as a fraction; if Plevel > 1 this value is interpreted as > a percent. > > http://skuld.bmsc.washington.edu/raster3d/html/rastep.html > > -Dave > > > On Dec 12, 2008, at 10:27 AM, Tom Goddard wrote: > >> 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 >>> >

2 1

making ribbon representaiton
by Bala subramanian 13 Dec '08

13 Dec '08

Hello all, I have a pdb file of a RNA duplex containing only the Phosphate atoms. How to make chimera to draw the ribbon representation. This is possible in vmd by using Tube as graphic style but i want to know if i can make it in Chimera too. Bala

2 1

length of a curved alpha helix
by Anindito Sen 12 Dec '08

12 Dec '08

Dear All I was wondering as how can I measure the length of "curved" alpha helix. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

3 2

problems before even getting to the plate...
by Jon Kenniston 12 Dec '08

12 Dec '08

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

4 4

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 >

1 0

(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 **********************************************

3 2

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

4 3

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

1 0