- Chimera-users - RBVI Mailing Lists

Parsing a new 3D file format
by ros 05 Jan '15

05 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 02 Jan '15

02 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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Add reasonable bonds from command line
by Enrico Ronca 29 Dec '14

29 Dec '14

Dear Sir. I'm Enrico Ronca a post-doc researcher at the National Research Council of Italy in Perugia. I'm contacting you because I often work with metal atoms and not always chimera show me bonds. I solved the problem removing all bonds and pseudo bonds and adding "reasonable bond between selected atoms" in the adjust bonds menu of chimera. Is there a way to run the same procedure from the command line so that I could automate it by a script? Thank you in advance for your reply. I'm looking forward to hearing from you Enrico

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Re: [Chimera-users] Customizing Chimera
by Eric Pettersen 25 Dec '14

25 Dec '14

On Dec 22, 2014, at 1:08 AM, Michał Kadlof wrote: > Hello, > > I'm currently work on proteins with disulfide bonds. I'm very often do the same sequence of tasks in Chimera: > > 1. open structure > 2. Select -> chemistry -> functional group -> disulfide > 3. extend selection to have selected all atoms of Cys-Cys bridge > 4. Show selected atoms > > Is there any way to wrap it into one-click button on toolbar? Hi Michał, While it is literally possible to put what you want on the toolbar, it's a bit easier to make a menu item instead. To do that, you create a command alias for the actions, and put that in a file that Chimera reads at startup so that it is always available. Details: The alias would be alias ^showbridge sel disulfide; sel up; disp sel This creates an alias named "showbridge" which is only expanded if typed at the beginning of a line -- that's what the ^ indicates. Such beginning-of-line aliases are also placed in an Aliases menu that appears after the Favorites menu (if you have any such aliases). To get the alias read by Chimera at startup you would put it in any of the files listed in the "Files to read at startup" section of the Command Line preferences (Favorites->Preferences). This is also described in more detail here: Command Line. Finally, if you really want it on the toolbar instead, that will involve making your own (simple) plug-in in Python. I can provide more detail about that if you like. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Can't open the CASTp site
by Lei Jinmin 18 Dec '14

18 Dec '14

Hi, I have to use CASTp tool for research sake, but I can't open the site anymore( http://sts-fw.bioengr.uic.edu/castp/index.php ). I remember it worked a couple of weeks ago. Does anyboday know when it begins working again? Thank you in advance! Best, Jinmin Lei Researh assitant Aalto University, Finland

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constrain measurement of rotation to a particular axis?
by Elaine Meng 18 Dec '14

18 Dec '14

Begin forwarded message: > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] constrain measurement of rotation to a particular axis? > Date: December 18, 2014 11:07:57 AM PST > > I think the sensible thing is to report the hinge angles without trying to use a common rotation axis. I can think of different ways to define the common rotation axis (you have to align all the structure in some way, then say how much the observed rotation about the axis for a particular structure translates into a rotation about a slightly different common axis), all of them arbitrary and hard to explain, and even harder to compute, so I wouldn’t go that way. > > Tom > >> From: Oliver Clarke <olibclarke(a)gmail.com> >> Subject: [Chimera-users] constrain measurement of rotation to a particular axis? >> Date: December 17, 2014 2:36:45 PM PST >> To: Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> Hi all, >> >> When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? >> >> I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. >> >> Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... >> >> Best, >> Oliver. >>

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How to change colour of H-bond between atoms
by Mahendra B Thapa 18 Dec '14

18 Dec '14

Dear Chimera Users, There is a hydrogen bond between, say, H20 of a ligand (LIG,res no: 240; this H-atom is attached with N atom of LIG) and O atom of GLU 120 residue. There are other hydrogen bonds too, but I am interested to change the color of that H-bond only to, say, red. I tried some like bondcolor red :240@H20 But, it is not working. Any suggestion might help me. Also, is there any way to change width of the H-bond? Thank you, Mahendra Thapa University of Cincinnati,OH

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constrain measurement of rotation to a particular axis?
by Oliver Clarke 17 Dec '14

17 Dec '14

Hi all, When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... Best, Oliver.

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Re: [Chimera-users] Request for Source code
by Elaine Meng 16 Dec '14

16 Dec '14

Dear Jayaraman T, You can turn off helical correction and mass weighting using command options, for example with this command: define axis perHelix true helicalCorrection false massWeighting false See: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I’m just trying to convince you this is the easy way! However, you already also have the source code in your download, as Eric described in his reply: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-December/010574.html> Best, Elaine On Dec 15, 2014, at 6:57 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > Yes Elaine, > > We can use Chimera but there are helical correction and mass weighting options exist. And am trying to get it done for all these helices without these options. > > Anyway let me follow up and write you back if there is a need of further assistance. > > I think it would help us more and thanks again for your kindness. > > Good day. > > On Tue, Dec 16, 2014 at 6:51 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Jayaraman T, > Chimera download already includes the Python code, but why not just use Chimera? It seems like that would be much, much easier than trying to find and understand all the parts of the code to do it. You can script it with Chimera commands “define” to create helix axes cylinders and “angle” to measure the angle between any pair of those. > > See: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> > > …and information on looping through structures: > <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 14, 2014, at 6:25 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > > > Dear, > > I'm Jayaraman T pursuing PhD here in Pusan National University. Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and please help me out at your earliest convenience. > > Thanks > > > > -- > Regards > > > Jram | 201493155 > PhD Student > Bio molecular Engineering Lab > School of Chemical Engineering > Pusan National University. > 30 Jangjeon-dong, Geumjeong-gu, > Busan, South Korea - 609-735. > +8210 9906 3680 > jram(a)pusan.ac.kr >

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