January 2015 - Chimera-users - RBVI Mailing Lists

Distance Grid SES calculation available?
by Hurt, Darrell (NIH/NIAID) [E] 06 Jan '15

06 Jan '15

Hi Chimera friends, This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). Is there some way to call the routine, especially in a script? Python maybe? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Parsing a new 3D file format
by ros 06 Jan '15

06 Jan '15

Hello! I would like to ask for advice and starting directions to be able to parse a new file format in Chimera so I can use Chimera's tools and generate images. The file format that I want to be able to open is generated from the Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) The AIMAll program of course can also do visualization and is very good at it. I am attaching an example of how a molecule looks. The problem is that if you want to work with big biomolecules (like DNA), the program is not very good to cloak/hide/select atoms so you have to click atom by atom to hide it and make some sense of the visualization. So, I will try to make a parser (or something that you would recommend) to open the file in Chimera and use Chimera's masking rules to select/deselect, hide/show atoms, which is very powerful. The text output generated by AIMAll has an XYZ list for each atom like this: Nuclear Charges and Cartesian Coordinates: ------------------------------------------------------------------------------- Atom Charge X Y Z ------------------------------------------------------------------------------- C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 That is easy, I think. But as you can see from the attached image, I want to be able to visualize the green spheres (which are called critical points and represents special properties of the electron density, extracted from quantum mechanical calculations). Those points are represented in the output file as: CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 -9.60854463947958E-01 Type = (3,-1) BCP C1 C3 Rho = 2.4067790431E-01 GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 3.5682199801E-01 HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 7.8991714842E-01 HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 6.1321358320E-01 DelSqRho = -5.2432458207E-01 Bond Ellipticity = 1.0071370222E-02 V = -2.5219393995E-01 G = 6.0556397216E-02 CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 1.96757752864282E-18 Type = (3,-1) BCP H4 C1 Rho = 2.9524693796E-01 GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 4.1039750300E-01 HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 0.0000000000E+00 DelSqRho = -1.1711322730E+00 Bond Ellipticity = 9.3591342377E-03 V = -3.7782718105E-01 G = 4.2522056404E-02 etc etc etc First line indicates the critical point number followed by the XYZ coordinate of the point, and the second line shows which atoms are involved between that critical point. The rest is the electronic properties of the critical point (nothing to visualize there) So, I am guessing that the critical points can be represented as dummy atoms in Chimera following the XYZ coordinates? The idea is that first the molecule coordinates are parsed and the molecule is displayed and then display the critical points of each atom. If possible, show lines joining atoms that have a critical point between them... I know it is a difficult task, but maybe you can provide some starting directions? Anything will help because right now is double clicking 1000+ atoms! Thank you so much and have a good day, Rodrigo. ------------------------- Rodrigo Galindo-Murillo, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)

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WebGL viewer
by Thomas Hrabe 05 Jan '15

05 Jan '15

Hi everyone, I am trying to implement a EM density viewer in a HTML page based on the chimera webgl & html export feature. The original page chimera exports when you save a webgl / html scene has been modified to load multiple JSON objects with densities as they come from chimera. The bar at the bottom of the page essentially performs a coarse density sliding similar to chimera. Almost all works great but what I am missing is how to connect the rotation that was applied to one model and to propagate it to all other models. What is happening now is that when one rotates one model and slides the bar, the next model will not be rotated but will be in it’s original position. Here’s my page I am currently working on http://localize.pytom.org/php/displayWebGL.php?jobID=tutorial I tried catching the mouse event with a loop, but it seems it fails to propagate the rotation to the other models. Check the block at line 916 in the code try { var rotMat = vsphere(mouse_position, new_position); var camera = this.camera; var matrix = new Mat4; matrix.$translate(camera.target[0], camera.target[1], camera.target[2]); matrix.$mulMat4(rotMat); matrix.$translate(-camera.target[0], -camera.target[1], -camera.target[2]); for (var i = 0, models = this.scene.models, l = models.length; i < l; ++i) { var elem = models[i]; elem.matrix = matrix.mulMat4(elem.matrix); } } Thank you in advance for your help, Thomas

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mmaker usage with md-movie perframe
by Bala subramanian 03 Jan '15

03 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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