- 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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features to be removed
by Elaine Meng 09 Dec '08

09 Dec '08

Dear users, The following features are slated for removal from Chimera after release 1.3. There will be a comment period of a few weeks before the features are removed, so please let us know as soon as possible if you deem any of these important to your work: * DelphiController * FreeBSD port * Keyboard Shortcuts * Lenses * Minrms Plot * Model Loops * Phantom Force Feedback * Selector Construction Panel * Surfnet * named volume subregions in Volume Viewer * precomputed volume subsamples in Volume Viewer * coloring capabilities in ResProp (will still be able to create/ modify amino acid categories) * the low-resolution display option in Side View (will always show the mini-view at high resolution) This list also appears in linked form at: <http://www.cgl.ucsf.edu/chimera/removepost1-3.html> The Chimera Team

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mclip slabs for multiple axes
by David A. C. Beck 09 Dec '08

09 Dec '08

I would like to be able to setup multiple per model clipping planes on different axes at the same time. As an example, mclip slabs from 0 to 10 angstroms on each axis simultaneously to reveal just those atoms in the 0,0,0 to 10,10,10 space. Is there a way to do this that I have missed? Maybe with another tool or the gui? I originally imagined that I would be able to do is something like this where mclip leaves any existing mclips until cleared with ~mclip #model. # clear all existing clipping planes ~mclip #0 # stack the clipping planes to reveal just the box 0,0,0 ... 10,10,10 mclip #0 slab true thickness 10 axis x mclip #0 slab true thickness 10 axis y mclip #0 slab true thickness 10 axis z But each successive call to mclip clears the previous per model clipping planes. Thanks, - David -- David A. C. Beck, Ph.D. dacb(a)u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle

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Chimera release 1.3
by Elaine Meng 09 Dec '08

09 Dec '08

Hello everybody, A new production release of Chimera (version 1.3) is available: <http://www.cgl.ucsf.edu/chimera/download.html#production> Release 1.3 addresses Microsoft Windows graphics drivers problems, particularly with integrated graphics accelerator chips. Versions are available for all platforms, including Mac Aqua (does not require X windows). Changes since the previous production release in July 2008 include: * Color Key tool * can read CASTp pocket data from local files * can write AMBER prmtop files, DMS dot surface files * more choices of charge parameter sets * can copy/combine molecule models * sequence alignment editing undo/redo * improvements in Axes and Build Structure * improvements in volume plane display, including ability to show contour lines * faster and more efficient solid volume rendering For details and the complete list, see the release notes: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.3.html> Enjoy! The Chimera Team

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Re: [Chimera-users] Making Hydrogen Bonds
by Eric Pettersen 09 Dec '08

09 Dec '08

On Dec 5, 2008, at 4:11 AM, Ahir Utsav Pushpanath wrote: > Hello. I was wondering whether you could tell me whether there is a > graphic/command line option enabling me to create "hydrogen bonds" > between my specific residue+ligand only. Or, whether it is possibly > to manually draw hydrogen bonds between atoms. In addition, using > the FindHbonds tool, is it possible to find H bonds between only > ligand + a specific type of residues, for example hydrophobic or > valine etc. Hi Ahir, What I would do if I were you would be to select the residues you care about along with the ligand, then in the FindHBonds tool check the "Only find H-bonds with" box and change the menu to "both ends selected". This will find only H-bonds completely contained in your selection. This may find a few H-bonds you don't want: ones between the non-ligand selected residues, and ones within the ligand itself. You can select the ones you don't want, and bring up the Selection Inspector (by clicking on the green button at the lower right of the main Chimera window) and change "displayed:" to "off". [control- double clicking on an H-bond will also bring up the Selection Inspector for it] Another alternative is to open a second copy of your structure. Select the residues you want in one model and the ligand in the other. Then do the "both ends selected" thing like in the above paragraph, but also change "Find these bonds:" (upper right of the FindHBonds dialog) to "inter-model". Then you will only get H-bonds between your selected residues and the ligand and no extra H-bonds. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Display all rotamers
by Elaine Meng 08 Dec '08

08 Dec '08

On Dec 6, 2008, at 9:35 AM, daniel.hilger(a)lrz.uni-muenchen.de wrote: > > I´m really sorry for my imprecise question. I will concretize it. I > know > the rotamer tool, but I don´t want to replace only one rotamer into > another. I will have them all in the structure and in the according > pdb-file. With the rotamer tool, it is only allowed to choose one > rotamer > out of the rotamer list before clicking "Apply". This is my problem, > and I > didn´t found an appropriate answer in the manual and help menu. Hi Daniel, I'm sorry for misunderstanding - It's true that Apply only puts one copy in the structure, but if you don't Apply and simply keep the Rotamer list dialog and choose all of its lines, that displays all of the rotamers at the same time. Maybe that would allow you to do what you want. The Rotamer list dialog allows calculating clashes and H-bonds, plus selecting the rotamer atoms so you can control their appearance with the Actions menu. The issue is that the structure can't have multiple indistinguishable atoms (with the same name and residue number). We have talked about allowing multiple rotamers to be applied to the structure by giving them different "alternate location" ID codes, but that has not been implemented yet. Also, some residues may have more rotamers than the number of possible alternate location ID codes. Nevertheless we will make sure it is on one of our requested features lists. So currently you can't save PDB with multiple rotamers, but you can save/restore the session in the state where all of the rotamers are displayed. I hope this helps, Elaine

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SpaceNavigator with Linux
by Juan M Vanegas 08 Dec '08

08 Dec '08

Hi, I just purchased a space navigator and would like very much to get it working with Chimera on linux. I don't know if you are aware of the spacenav project (http://spacenav.sourceforge.net/) it is a GPL alternative to the proprietary drivers. I would be willing to help with some of the coding/testing, I know a little bit of programming and I have the device. Thanks for the great work with Chimera. Cheers, Juan

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Named selection for subset of markers
by Giovanni Cardone 08 Dec '08

08 Dec '08

Hi all, I am trying to save a selection of a subset of markers as a named selection. However, the named selection results empty: is it a normal behavior? I am using Chimera version 1 build 2552. Thanks in advance, Giovanni

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chimera startup problem
by Jinzhong Lin 08 Dec '08

08 Dec '08

Hi, I installed lastest chimera build (1.3.2576) on 32-bit linux platform. When I ran chimera I got for following error message Traceback (most recent call last): File "/opt/sciencetools/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/opt/sciencetools/chimera/share/chimeraInit.py", line 361, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "/opt/sciencetools/chimera/share/chimera/tkgui.py", line 2520, in initializeGUI master.tk.call('tix', 'initstyle') _tkinter.TclError: expected integer but got "9.5" Can anyone help me out? P.S. I opened the tkgui.py file and comment line 2520: master.tk.call('tix', 'initstyle') Chimera start without the error and seems usable, But I am not sure if this is appropriate. Best, lithlin

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Maintaining Color and Formatting Selections for New Molecules
by Eric Ganz 08 Dec '08

08 Dec '08

Now that I have formatted and colored one molecule, I would like to maintain the color and formatting selections for a series of new molecules. How should I do this?

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Re: [Chimera-users] Labeling the surface representation
by Elaine Meng 07 Dec '08

07 Dec '08

Hi Mehdi, I misunderstood your question. I thought you meant the atomspec balloons that temporarily pop up when you put the mouse over the atoms, and the previous instructions apply to those. Your picture shows the regular residue labels. To show a residue label, the residue's ribbon or some of its atoms must be displayed. It is OK for the surface to also be shown, but then the problem is that the surface usually covers up the residue labels so you can't see them. You can make the surface transparent to see the labels inside (see "Actions... Surface... transparency..." in the menu or use the command "surftransparency"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surftransparency.html > If you are displaying these labels to make a figure, another suggestion is to use 2D Labels. You have to enter the text of a 2D label yourself, but you can move it to any position in the window. 2D Labels are independent of the structure and how it is displayed. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… > Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 7, 2008, at 11:31 AM, Mehdi wrote: > Thank you for your detailed information. I could not still figure > out how to label the residues on surface representation. I have > attached the figure (for instance) showing the ribbon representation > with a few amino acids labeled but if I want to achieve the labeling > on the surface the labels,unlike the ribbon, do not appears on it. I > also followed the tutorial but the atomspec balloons were not > observed on the surface as soon as the ribbon or simple stick > representation are hided.Do I have to keep the simple bond or ribbon > representation in order to keep the atomspec balloon and labels > observable?

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show CA as sphere and ribbon
by lvyuan zhang 07 Dec '08

07 Dec '08

Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

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I got it.
by lvyuan zhang 07 Dec '08

07 Dec '08

I saved the CA atoms as another pdb file, and then import it, and show atoms as sphere. ________________________________ From: lvyuan zhang <gleanerly(a)yahoo.com> To: chimera-users(a)cgl.ucsf.edu Sent: Sunday, December 7, 2008 4:42:20 PM Subject: show CA as sphere and ribbon Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

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Labeling the surface representation
by Mehdi 07 Dec '08

07 Dec '08

I am a new user of chimera, I would like to know how to label the residues in surface representation like the same action for ribbon! It simply works for ribbon but unfortunately I could not get it to work for surface. Mehdi

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The Macromolecular Modeling Blog
by Nir London 06 Dec '08

06 Dec '08

Hi all, We've started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/ We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears. On its background there is an image of a protein-protein complex I've created using chimera, can any of you suggest a nicer figure for the background ? The best image anyone will send me will be used as background (with due credits :) please check it out and tell me what you think... Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com

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Image use permission request from Jones and Bartlett Publishers in Boston
by Asuka Ohsawa 05 Dec '08

05 Dec '08

Dear Sir or Madam: My name is Asuka Ohsawa, and I am a freelance photo researcher for Jones and Bartlett Publishers, Inc., in Boston, MA. We're currently working on an educational textbook by Dr. Benjamin Lewin titled Essential Genes, 2nd Edition, and the author has requested to use the image that appears on the following website: http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/rnabases/ rnabases.html At your earliest convenience, could you please let me know who owns the copyright to the image in question, and how I can get in touch with him/her? In order for us to publish the image properly, we need to acquire a signature from the author of the image. Your kind assistance in this matter will be much appreciated. Should you have any questions or require additional information, please do not hesitate to contact me. Thank you, and I look forward to hearing from you. Best, Asuka Ohsawa Freelance Photo Researcher Jones and Bartlett Publishers, Inc. Email: asukabunny(a)gmail.com Phone: 718/349-0393

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"docking" animation
by Elaine Meng 05 Dec '08

05 Dec '08

On Nov 19, 2008, at 9:37 AM, Bagchi, Angshuman wrote: > Hi, > Could you please tell me how to produce animation in chimera. > Actually, I have 2 proteins and would like to represent them as they > are getting docked. What I mean is that I would like to move the > proteins and then show that as if they are getting docked. Can this > be done with chimera? > Thanks > Ang Hi Ang, Yes, it can be done. Here is how I would do it: (1) create a Chimera session that includes saved/named positions of the proteins separated and the proteins docked. (2) figure out a set of commands that does the stuff you want in your animation, which would include "reset" to gradually change from one saved position to the other; put the commands in a file. Just opening the file will execute the commands. (3) after you are happy with what the Chimera command file does, just put a "movie record" command at the top of it and a "movie encode" command at the bottom, and execute it. Now with more details: (1) Open the structures of the two proteins from two separate files so that they can be moved separately. You can "freeze" a structure by deactivating it, so that the mouse moves only the other structure: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html#activedef > Save at least two positions, one with the proteins separated, another with the proteins docked together, as you want them to appear in your animation. The current position is saved using the command "savepos": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/savepos.html > You could even save multiple positions for more control over the path the proteins will take as they are "docked" in the animation. There is a nice example in the online movie-making tutorial, see the "Ligand flying into unbound conformation" section: <http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html> Get the display how you want it: background color, ribbons, ribbon style, which atoms are shown, atom display style, colors, etc. See "tips on preparing images": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#tips> You might also want to add a title using 2D labels (if so, leave room for it when you save the positions). <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2… > Save the session (File... Save session As). It will include your saved positions and any 2D labels. Now you could exit and later restart the session without losing your work. (2) You could either try out commands by typing them individually, or by putting them in a text file (named *.com or *.cmd) and repeatedly opening the file after you adjust its contents and going back to the starting position. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#c… > The "reset" command is used to go from one saved position to another. It can be done abruptly in one frame or gradually over a specified number of frames. See movie-related commands for links to the manual page of "reset" and other commands that can do things over a specified number of frames. Besides the "reset," you might want to do other things like translate or rotate or fade in/out 2D labels with these commands. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#movieco… > There are also links to a few example movie command files on that page. (3) Once you are happy with what the script does when you open it, then you can put a "movie record" command at the top and a "movie encode" command at the bottom. See the example movie command files and the "movie" command description: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html > I prefer this process because at the end you have a session file and a command file that allow you to either reproduce the process efficiently, or to make some small change without a lot of duplicated effort. I am told that "reset" has had some problems which were just fixed, so if you get a bad behavior using that command, try getting a recent daily build from <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> I hope this helps, 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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Chimera on Linux PPC
by Tom Goddard 05 Dec '08

05 Dec '08

Hi Justin, We do not currently build Chimera for Linux with PowerPC processors. Chimera includes more than 30 third-party libraries which we build automatically on each supported platform (Windows, Mac, Linux...). Compiling all those libraries is the real problem. Many of those libraries require special patches to build on all our platforms (Windows, Linux, Mac). It would likely take weeks of work for Linux PPC for someone very experienced in compiling open source packages from source code. We do not have the resources to do that for such an obscure platform. The next platform we will likely support is Mac 64-bit (Intel) sometime in the next year, after that 64-bit Windows. The latest Chimera can be compiled without the proprietary molecular surface code. We don't have that latest source code on the web site, but if you manage to build all the third-party packages (called "foreign" packages on our source code download page) I'd put the latest source code on the web and tell you how to disable the molecular surface compilation. Tom Justin A. Lemkul wrote: > > Dear Sir, > > I am installing a few machines in our lab that are running Ubuntu > Linux (8.04) on PowerPC architecture. They are iMac G5 desktop > machines, a little old, but new to us. I have thus far been unable to > install Chimera on these machines, being that it is such an odd setup, > and PPC is rapidly falling out of use. I came across a message in the > chimera-users archive that made me wonder if installing Chimera on > these systems was even possible: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000607.html > > Are you aware of anyone that has installed Chimera on such a system? > Do you think it is even possible? We would really like to be able to > use Chimera on these machines (it is installed on all our other > machines, and has become a staple in our lab). Any advice you could > give me would be greatly appreciated. > > If I can resolve all of the dependencies, would Chimera install > without MSMS? I don't believe I can install MSMS on these machines, > given the available installation packages. > > Thank you very much for your time and attention. > > -Justin >

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Vista Video Card Error
by Devon Cayer 04 Dec '08

04 Dec '08

Hello, I'm currently attempting to model some viral capsid proteins using your software. Unfortunately, when I attempt to use the "side view" option I get a video card error, and I'm told to update my video card drivers. I've contacted the manufacturer and they have told me my laptop, a Gateway MT6821, is up to date with all the latest drivers. What else could be a possible problem do you think? I look forward to any input, Sincerely, Devon C Devon M Cayer Graduate Student The Scripps Research Institute Ghadiri Lab devcayer(a)scripps.edu

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building a alpha helix
by Anindito Sen 04 Dec '08

04 Dec '08

Dear All I was wondering if there is any tool by which can generate an alpha helix, as an extension of a truncated crystal structure docked in the density map. The possibility of the truncated portion of the protein behaving as an alpha helix has been predicted by different groups. The density map shows some empty regions (after the crystal structure has been docked) just good enough for an alpha helix to fit in. Best 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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Transparency of ribbons
by lvyuan zhang 04 Dec '08

04 Dec '08

Hi all, I'm a new user and my question maybe a little weird to you guys. I want to make some parts of my protein, let's say "A", partially transparent, so when compared to other parts of the protein, let's say "B", these "A" parts are hardly visible (the background is white). So I set the alpha value of "A" to less than 1, such as 0.1. then I save the image with POV-ray. The resulted "A" is too dark, and it is still quite "visible". Is there any way to make partially transparent ribbons lighter, instead of darker than non-transparent ones? I would really appreciate it if any one can help resolve this problem. Thans! Cheers! Luyuan Zhang

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Software(Drug Design)
by Tarit Mitra 04 Dec '08

04 Dec '08

28, Ashfield Green Yateley Hants GU46 6AL UK Dear Sir, I am a retired scientist, and working on an honorary basis for the University of London. I work from home and go to the University in regular interval. I would very much like to use your software for drug design. I was wondering whether you would grant me a free academic licence to the software. I shall only use the software for academic purpose and not for any financial reason whatsoever. I have both Linux(Ubantu) and Windows XP. My computer has 40GB hard disk with 756MB RAM I shall be grateful if you will kindly consider my case favourably. Yours faithfully T. K. Mitra, B.Sc(London), Ph.D(London)

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opaque background
by Mueller, Juergen-Joachim 01 Dec '08

01 Dec '08

Dear all, is there a possibility to make the background invisible to be able to overlay a structure over anything? Thanks, Juergen

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Chimera rotational matrix
by Bui Khanh Huy 01 Dec '08

01 Dec '08

Hi, I notice that Chimera has slightly different in calculation of transform when I tried to rotate my EM density (200x200x200 mrc file) using Chimera. The origin of the density reported by Volume Viewer is 0,0,0 First, I print out the homologous transform matrix using: >>> om = chimera.openModels >>> mlist = om.list() >>> m = mlist[0] >>> print m.openState.xform The transformation is: 1 0 0 0 0 1 0 0 0 0 1 0 If I rotate the model using command: roll z -30 1 Then print out the transform matrix again: 0.866025 0.5 0 -36.8852 -0.5 0.866025 0 61.2937 0 0 0 1 That would be weird because I didn't do any translation. So what is really happening in Chimera when I rotate the model? Best, Huy

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How to generate submodels in a mol2 file in Chimera?
by CHIU,YEUNG 01 Dec '08

01 Dec '08

Dear friends, Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know). Thank you for your help and sorry to bother the others. Best wishes. Sincerely yours CHIU,YEUNG

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Increases size of labels
by Todd Weaver 25 Nov '08

25 Nov '08

Under the Actions pulldown for Label --> Other is there a way to increase the size of the lettering/numbering. When I make side by side stereo the labels are too small for publication. Thanks so much! -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281

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