- Chimera-users - RBVI Mailing Lists

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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