- Chimera-users - RBVI Mailing Lists

ubuntu graphics problem
by Elaine Meng 23 Dec '08

23 Dec '08

Fabian reports a Chimera/ubuntu problem and a solution: Begin forwarded message: > > Hi Elaine, > > To save people painful dealing with the newest version of ubuntu, > 8.10, if everybody asks you, chimera has an incompatibility with the > "desktop effects" and "compiz" effects of this version. The only > solution I found (after two days of trials) is to remove compiz (apt- > get remove compiz) and completely disallow the desktop effects > (through system settings). > > Best regards, > Fabian > >> Something more urgent, I have recently updated my kubuntu system to >> 8.10, and the nvidia graphics card to nvidia-glx-177 (177.80 to be >> precise) which should be the correct one. The problem is that after >> a few seconds of working with some molecule in the chimera window >> (which opens fine), it gets stuck and works very very slowly if at >> all. That is a problem since I use chimera very heavily. Any hint >> you could give me of how to solve the problem would be invaluable. >> Just to mention that I have heard of problems with this version of >> kubuntu, but surely there is a workaround. >>

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anti-aliasing in mac version
by Grigore Pintilie 22 Dec '08

22 Dec '08

If I'm not mistaken it looks like anti-aliasing is not used in the mac build of chimera... is there a way to enable this? I'm using a Macbook pro with the nvidia card and Mac os X. Greg

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NMR-Style structures
by Eric Pettersen 18 Dec '08

18 Dec '08

On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote: > Is any way for Viewdock in Chimera to open a pdb file with NMR-style > structures so that I can view those NMR-style structures one by one? Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal. Another possibility is to open the NMR file as a trajectory (MD/ Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function. You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster. It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Stereo view
by Eric Pettersen 18 Dec '08

18 Dec '08

On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote: > Another question is how to see a stereo view of a structure in > Chimera. Do I need a pair of special glasses for that? You can use the Camera tool (Stereo) to make Chimera show either a cross- or wall-eyed stereo view. You don't need special glasses to use those modes, but you do need to be able to cross or unfocus your eyes (respectively) to get the two images to merge. Some people have difficulty doing that. The other stereo modes mentioned on the page I linked to do require special glasses, and are described in detail on that page. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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info about energy in the minimize module
by Bruno Villoutreix 18 Dec '08

18 Dec '08

Hello not sure this is the right place to ask... when running minimization in Chimera, do you have a window that show the energy values before and after the process ? or should this be done via a terminal window using the nogui option ? maybe the info is here around but could not find it so far many thanks Bruno

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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

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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

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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 >>> >

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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

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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

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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

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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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Generated density maps
by maya shcushan 10 Dec '08

10 Dec '08

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

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generating a density map
by William Jeffrey Triffo 09 Dec '08

09 Dec '08

hello, I remember seeing a pdb-to-density-map discussion at some point on this mail list, maybe using something from the EMAN package (pdb2mrc or something like that)? At any rate, a colleague recently asked me if I knew a way to generate a density map from point-cloud data that he has. This sounds a lot like the same question, except his data is anisotropic in z, so instead of assuming an isotropic/spherical gaussian around point centers, he has different sigmas for x/y and z. Does anyone have an algorithm he might be able to use to generate an MRC map from this kind of data? He is wanting to do some volume visualization, but to use Chimera he would need some sort of volume map (such as MRC). thanks for any advice on this, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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savepos/reset
by Matthew Dougherty 09 Dec '08

09 Dec '08

Let's say I have 5 models and I save a number of positions (savepos). Then I later create some morphs between the models. When I do a reset of a position, the morph model's position does not correspond with the other model positions. This is partially due to the method of camera control in chimera of moving the models and keeping the camera position pointing in the z direction. Is there a way to incorporate the morph model into the saved positions that were created prior to the creation of the morph model? having similar problem with models I open after the positions are saved. thanks, Matt

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limits of transparency?
by lvyuan zhang 09 Dec '08

09 Dec '08

Hi, I'm making my protein ribbons partially transparent by changing the alpha value in color editor. I tried a=0.2 and a=0.05, and I found that after raytracing, there is no difference between these two. Isn't a=0.05 supposed to be more transparent? Is this a bug or something is wrong with some settings in chimera that I don't know? Thanks a lot first! Cheers! Luyuan Zhang

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