- Chimera-users - RBVI Mailing Lists

saving with angles
by Gabor Papai 12 Dec '06

12 Dec '06

Dear everybody, Is there a way in Chimera to save density maps when I rotate them with the modified angles? In practice, I use the 'fit map in map' to align two maps in respect to each other and I would like to save them for further analysis with different softwares. Therefore I would like to conserve their position (shift and rotation). Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Delphi Controller
by sette＠uniroma2.it 11 Dec '06

11 Dec '06

Dear all, I have a simple question: does Delphi controller works under unix only or it is possible to work with it under Linux and/or Windows XP? Thanks a lot, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Read compressed PDB files -question, suggestion
by Moo Cow 08 Dec '06

08 Dec '06

We store the PDB locally, but compressed. Can one persuade chimera to read coordinates from a pipe ? Maybe this could be done at the python level. It might also not be too hard to use the python binding to the zlib library, but I would not know how to do this. I imagine the interest (or not) would not be limited to reading PDB files. many thanks for any suggestions. -- Search for products and services at: http://search.mail.com

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Apply the symmetry to the fitted models in map
by Hong-Wei Wang 06 Dec '06

06 Dec '06

Hi, Tom I remember you were showing docking a model into map with high symmetry (you showed the actomyosin filament example). I am wondering how you generate the symmetry in the docking and if the symmetry information is necessary for the correct fitting. Thanks a lot! Hongwei ----------------------------------- Hongwei Wang, Ph D MS 20A-355, LSD, LBNL 1 Cyclotron Rd, Berkeley, CA 94720 510-642-2222 (O) 510-642-8806 (FAX) hwwang(a)lbl.gov

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volume viewer issue
by Matthew Shawkey 06 Dec '06

06 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 29 Nov '06

29 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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