- Chimera-users - RBVI Mailing Lists

volume viewer issue
by Matthew Shawkey 07 Dec '06

07 Dec '06

Hi, I am using chimera to visualize a stack of EM serial sections. I can load them into Chimera (as MRC file), but when I try to view the stack in the volume viewer w the "solids" option all I see is a white square.. w the mesh and surface options the stack shows up as a grainy image on which it's difficult to see any depth.. any suggestions? THanks, Matt

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Uploading several trajectories for MDmovie
by Anna Feldman-Salit 04 Dec '06

04 Dec '06

Dear all, I would like to know if there is any possibility to sequentially upload several trajectories with MDmovie option (or command line) and then to visualize them with "no stop" in between. These trajectories were generated by AMBER with "restart" input files. Such an option happens to be in VMD, but it's more convenient for me to work with Chimera (I have Chimera1.2304). Thanks a lot in advance, Anna

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Fit models to map
by hsosa＠aecom.yu.edu 04 Dec '06

04 Dec '06

I wonder how the "Fit models to map" function do the fitting. Does it find the best cross-correlation value between a 3D density calculated from the atomic model and the 3D density map?. What is the maximum displacements and rotations tested around the current position? What is the step size of the rotations/displacements? Thanks Regards Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] inter-surface calculations in Chimera
by Elaine Meng 01 Dec '06

01 Dec '06

Hi Gali, Eric forwarded your question to me. The Intersurf tool generates a surface between the interacting molecules that is different from the surface of either molecule - it is mainly useful for viewing an interface and showing its properties (for example, with coloring by hydrophobicity or electrostatic potential), but not for measuring the surface area. It is possible to measure volume and surface area in Chimera, but currently it is a long process. We hope to have a simpler process available in the future. I'll describe two different approaches. (1) the simpler and more approximate way to calculate buried surface area and void volume in the complex: approx buried surface area = [(surface area of X) + (surface area of Y) - (surface area of XY)] / 2 approx interface void volume = (volume of XY) - (volume of X) - (volume of Y) The "Measure Volume and Area" tool can be used to calculate the surface areas and volumes. [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/ measurevol.html ] The trick is to first make a surface that encloses both X and Y and measure its values. Then, make surfaces that separately enclose X and Y and measure again. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel command: surfcat complex :.a-d command: surf complex Tools... Surface/Binding Analysis... Measure Volume and Area (measure values for the complex) command: surfcat protein :.a-b command: surf protein (choose the protein surface in Measure Volume and Area, compute again) command: surfcat dna :.c-d command: surf dna (choose the dna surface in Measure Volume and Area, compute again) Finally, use the equations above. All the results can be viewed in the Reply Log (under Favorites). These values are for molecular surfaces (also known as solvent-excluded, where the probe touches), not solvent-accessible (traced by the probe center). For this structure, I calculate approx 530 square angstroms surface area buried, approx 730 cubic angstroms of interface void volume. (2) A more detailed approach can yield different values for the areas buried on X and Y: (surface area of X buried in the XY interface) = (surface area from all atoms of X in surface enclosing XY) - (surface area from all atoms of X in surface enclosing just X) with a similar equation for Y. Currently, the only way to get atomic rather than total surface areas in Chimera is by using the "Area/Volume from Web" tool [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html ] which uses a Web server at NCBI and loads the atomic values into Chimera. Because the MSMS option of the server has problems with nucleic acids, the only choice for your complexes is to calculate solvent-accessible surface areas (not the solvent-excluded surface areas calculated by method (1) above). The main trick is to first send only XY to the server (making sure solvent, ions, etc. are NOT included). Then using Attribute Calculator, [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html ] sum the values for the atoms of X in that combined surface, and likewise get a total for Y. Then, delete everything except X and send it to the server again, getting the total for X alone. Close/reopen the structure, delete everything except Y, and send it to the server to get the total for Y alone. Subtract the value for X (Y) in the complex from the total for X (Y) alone. Here is a concrete example. PDB structure 1cf7 has two protein chains A and B, two DNA chains C and D, and some water. I'd open the structure and delete everything but the protein and DNA. command: open 1cf7 command: select :.a-d command: sel invert command: delete sel Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein and DNA command: select :.a-b Tools... Structure Analysis... Attribute Calculator calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for A-B (which is the PROTEIN IN THE COMPLEX) (I get approx 7473) command: select :.c-d calculate an attribute (name doesn't matter) for "models" with the Formula: sum(atom.accessibleSurface) with the option "Restrict formula domain to current selection" write down the total for C-D (which is the DNA IN THE COMPLEX) (I get approx 4502) command: delete :.c-d now only the protein is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the protein - get the total for PROTEIN ALONE (Favorites... Reply Log) (I get approx 8842) command: close 0 command: open 1cf7 command: select :.c-d command: sel invert command: delete sel now only the DNA is left Tools... Surface/Binding Analysis... Area/Volume from Web - calculate "Accessible Surface (Gerstein)" for the "Molecule" which now consists of only the DNA - get the total for DNA ALONE (Favorites... Reply Log) (I get approx 5758) Use the equation above to get the buried solvent-accessible surface areas. I calculate approx 1369 square angstroms buried for the protein, approx 1256 square angstroms buried for the DNA. You can't compare these solvent-accessible areas to the solvent-excluded areas calculated by method (1) ... the solvent-accessible values are generally much larger. PHEW! I congratulate everyone who got this far. The written explanation makes it seem longer than actually performing the process. I hope this helps, Elaine On Nov 30, 2006, at 7:35 AM, galig wrote: > Dear Eric, > > I have a small question regarding the calculation of inter-surfaces in > Chimera: > I have several protein/DNA complexes, and I would like to compare > their protein/DNA interfaces. I used Tools-->surface/binding > analysis-->compute interface surface and chose the protein and DNA > chains. the result, if I understand it correct, is per atom. Is there > a place to find the overall number representing the contact surface? > is this a different or similar calculation? > One more thing- how do I calculate the void intermolecular volume > between the chains? > > Thank you and sorry to bother you, > > Gali Golan > Dept. of Inorganic Chemistry > The Hebrew U. of Jerusalem > Jerusalem 91904 Israel > Tel. 972-2-6585610 > Fax 972-2-6585319 > ----- 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

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Re: [Chimera-users] Chimera on x86_64?
by Thomas Goddard 30 Nov '06

30 Nov '06

Hi Ben, There's no technical obstacle to us making regular 64-bit linux Chimera distributions. The only issue is having time to do it. The work involves compiling the ~30 third party libraries that Chimera uses. I did this is the past and it took about one day of fiddling. Our Chimera build scripts compile all of the third party libraries automatically and my past hand fiddling to build on 64-bit linux would have to be put into our scripts. That could take a 1 to 5 days of work. We have a 64-bit linux machine to do the work on. So it all comes down to when one of the 4 developers (Tom Goddard, Eric Pettersen, Greg Couch, or Conrad Huang) has time to work on that. I don't think I will have time until January at the earliest. Could you give me a better sense of how much need there is in the Sali lab? Are you really saying you would not install 32-bit Linux system libraries except for Chimera? I would think there are a fair number of applications out there with binary distributions only for 32-bit. The other problem you point out is that 32-bit Chimera Python cannot use your own 64-bit Python modules. Are you using additional C Python modules within Chimera that do not come with Chimera? That is interesting -- what are they? Tom > From: Ben Webb <ben(a)salilab.org> > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: Wed, 29 Nov 2006 12:51:27 -0800 > Subject: Chimera on x86_64? > > I wonder if you could give me a rough idea of when you plan to make > regular builds of Chimera on x86_64 (if at all)? All I've been able to > glean from the download page and the mailing list archive is that you > do make occasional builds, but recommend the 32-bit version. > > Memory isn't so much of an issue for us in particular (although we are > increasingly looking at large EM maps) but the requirement to have > 32-bit libraries is starting to become a problem. All of our new > desktops are x86_64 machines, and it's a pain to require the 32-bit > libraries just for Chimera. Additionally, our users want to > mix-and-match Python modules (including Modeller, of course) and > Chimera is unable to import any module which has a C backend, since > they're compiled for x86_64 and the Python interpreter in Chimera is > 32-bit. (Of course, we could recompile all of our other Python modules > for 32-bit, but that would cause problems with x86_64 apps.) > > If you need people to test x86_64 Chimera builds, we certainly have > some demanding users here to break them. ;) > > Ben > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle

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Multiple Volume Viewer Windows and saving PDB file
by Batsal Devkota 28 Nov '06

28 Nov '06

Hi, I am just wondering if there is any way that I can have two or more volume viewer windows open at the same time. I am comparing two density maps and to be able to change the threshold and color for both maps, without having to go back and forth in the same window, would be much easier and useful. Also, I recently fitted a pdb crystal structure into a density map but was not able to save it with relation to the density map (the feature which was available in previous releases). However, if I have multiple pdb files open then I can save the pdb file of my interest with respect to the map. Is there anyway to save a fitted pdb file with respect to a density map without opening other pdb files? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

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Stereo on the 1.2304 version
by Anna Feldman-Salit 28 Nov '06

28 Nov '06

Hello, Unfortunately, I'm facing with a problem of stereo option on the version 1.2304. I can see the stereo when I turn the "stereo" option on, but the quality of the picture is not of the best ones. The main picture is likely screened on background, while it's also impossible to focus on the frontal part. I was playing a bit with camera-viewing parameters, but nothing worked for me. Before, working with pymol I used the "swap sides" option, which helped a lot. I tested our stereo glasses with pymol's stereo option again and it works smoothly. Since I definitely prefer to work with chimera, I would appreciate if this problem would be solved somehow. Do you have any suggestions? Thank you in advance! Best, Anna

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Re: [Chimera-users] Increase/decrease the sphere
by Eric Pettersen 28 Nov '06

28 Nov '06

I forgot to mention that if you want to control ball/stick size on a more permanent basis, you can use the New Molecule preferences (Favorites->Preferences) to set them for all new molecules you open. --Eric On Nov 27, 2006, at 9:21 PM, tuhin(a)iitk.ac.in wrote: > Thanks for your helpful suggestion, Eric. > > Regards, > TKP > >> Hi, >> Sphere size is the same as the atom's VDW radius. You can change >> atom radii with the "vdwdefine" command, or by selecting atoms and >> bringing up the Selection Inspector (click on the button at the lower >> right of the Chimera interface) and typing a new value into the >> "radius:" field. >> Ball and stick size are controlled on a per-model basis. Use the >> Model Panel (Favorites->Model Panel) and double-click on line with >> the model you want to control. A dialog listing the attributes of >> that model will come up. The "ball scale:" field controls the size >> of balls. It is a fraction that the VDW radius is multiplied by to >> get the ball size (default: 0.25). The "stick scale:" field controls >> stick size and also a fraction that sticks get multiplied by. The >> default stick radius is 0.2 angstroms and default stick scale is 1.0, >> so the final default radius is 0.2 angstroms. The help page for the >> attribute dialog describes why there are two numbers involved if you >> care, and also describes the other attributes if you're interested. >> >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >> pett(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu >> >> >> On Nov 27, 2006, at 6:56 AM, tuhin(a)iitk.ac.in wrote: >> >>> Dear Chimera users, >>> >>> Could anybody tell me whether there is a way in chimera to >>> increase/decrease the size of the spheres/ball-and-stick in atom >>> display >>> (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in >>> "wire >>> width", is there something like that for the above two options ?? >>> >>> Waiting for yours suggestions. >>> Thanks in advance. >>> >>> Best, >>> TKP >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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Control of the volume viewer from the command line
by Lukas Palatinus 28 Nov '06

28 Nov '06

Hello all, I am trying to make a movie showing an evolution of an electron density map during an iterative optimization. For each optimization step I have one density map as volume data in xplor format. I depict the maps using the volume viewer, where I can set the number and level of the isosurface thresholds as well as their color. However, each newly opened map opens with default threshold setting, which is not suitable for my purposes. I make the movie using a command file of the type: open density1.xplor movie record wait 10 movie stop close 0 open density2.xplor movie record wait 10 movie stop ... I would need to be able to control the properties of the isosurfaces of the newly opened map from the command line or from the script file, or find a way to preserve the properties set for the first map in all subsequently opened maps. The search in Chimera manual did not lead me anywhere. Could anyone give me a hint how to proceed? With best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 27 Nov '06

27 Nov '06

Hi Michael, Perhaps you can compare the orientation between the exact symmetric placement of a chain and the actual position by measuring the translation and rotation angle needed to align the two. By rotation angle I mean that any rotation can be represented as a rotation about a single axis (which depends on the rotation). I do not understand what you mean by rotation angles about x, y and z axes. As I mentioned that depends on the order of the rotations and therefore is rarely used. In the Chimera match command or matchmaker tool the optimal rotation matrix is computed -- it is *not* decomposed into separate x, y and z rotations during that calculation. I suppose if your system has symmetry about the z axis you could ask what rotation about z best aligns a chain with the exact symmetric chain location. In other words, only a z-axis rotation rather then rotation about an arbitrary axis would be allowed. Chimera does not have code for that and I have never heard that number reported. If you spell out precisely what angle is needed I can give better advice on how to get it from Chimera. Tom > From: "Stohr, Michael" <stohr(a)uni-mainz.de> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Date: Mon, 27 Nov 2006 09:51:31 +0100 > Subject: AW: Get angles in degree out of Rotation matrix > > Hi Tom, > > Thanks a lot for your description. It does not fit completely my demand. I will rephrase my question, is there a simple way to determine the three angles between the two 3d-structures of two identical chains? The background is that my molecule is not absolutely symmetrical and I want to quantify the asymmetry. So, I want to be able to say, this angle between this two chains differs from ideal symmetry angle by X degrees for different directions (x, y, z). I thought the rotation matrix would be the way to do so, but it does not seem so. I've found a not very precise method by using the distance tool and trigonometric functions. Therefore, if there is no answer for my question it will be ok at first especially I have to finish my theses very soon. By the way, in which order does for example the tool match or matchmaker rotates a structure or is this not predictable? > > Thanks for your afford, > Michael

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