- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] symmetric fitting
by Tom Goddard 07 Oct '08

07 Oct '08

Hi Sudheer, This means your GroEL map does not have the cylinder axis along z. When you press the Orient button in the volume dialog you can see the orientation, the screen horizontal axis is x, the screen vertical axis is y, and in/out of the screen is z. I've attached a Python script that can produce the symmetry matrices for different cylinder axes. You run it by opening it in Chimera and the output is seen in the Reply Log (Favorites menu). You'll need to edit the script to use the correct axis. Tom skmolugu(a)miners.utep.edu wrote: > Hi Tom, > I have used the matrix file you have gave me and could succesfully generate the coordinates file. After saving the pdb file with the new coordinates, I reopened the saved pdb file that has 14 subunits and it is turns out to be perpendicular to map that has been used. How can I avoid this problem? > thank you very much for your time, > sincerely, > sudheer. > ---------------------------------------- > >> Date: Mon, 6 Oct 2008 12:06:32 -0700 >> From: goddard(a)cgl.ucsf.edu >> To: skmolugu(a)miners.utep.edu >> CC: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] symmetric fitting >> >> Hi Sudheer, >> >> Figuring out the symmetry matrices for using the symmetric fitting >> capability >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcop… >> >> requires some work. First note that the symmetry matrices you want are >> those that transform (rotate and shift) the volume data to an identical >> configuration. >> >> Your case is 2 stacked 7-mer rings. Assuming the z axis is the >> symmetry axis of the map (need to set origin so the center of the >> cylinder is at xyz = 0,0,0 in the volume dialog Coordinates panel) you >> could just compute the needed rotation matrices >> >> cos(a), sin(a), 0 >> -sin(a), cos(a), 0 >> 0, 0, 1 >> >> Could write a script (python script attached) or use a calculator. Also >> you want to flip around x axis by 180 degrees to get 7 more rotations >> with the two 7-member rings exchanged. With that approach I get the >> following lines to add to the PDB file: >> >> REMARK 350 BIOMT1 0 1.000000 0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 0 -0.000000 1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 0 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 1 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 1 -0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 2 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 2 -0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 3 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 3 -0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 4 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 4 0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 5 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 5 0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 6 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 6 0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 7 1.000000 -0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 7 -0.000000 -1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 8 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 8 -0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 9 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 9 -0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 10 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 10 -0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 11 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 11 0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 12 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 12 0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 13 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 13 0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.000000 >> >> If your map origin is not the center of symmetry or an x-axis flip is >> not a symmetry then these matrices won't work. You can try to set the >> correct origin -- the right value can be found with some tricky use of >> the output of the Fit in Map tool, fitting one copy of the map into >> another copy. Or you could fit one copy of the map to another and use >> the matrixget command to output that symmetry matrix to a file, then do >> that for all symmetries to create the needed matrix text. >> >> As you see this process has not yet been made easy. >> >> Tom >> >> >> >> >> >> skmolugu(a)miners.utep.edu wrote: >> >>> HI, >>> In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. >>> thankyou, >>> sudheer >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> # Chimera script to print symmetry matrices for GroEL 14-mer. format = '''REMARK 350 BIOMT1 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT2 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT3 %3d %10.6f %10.6f %10.6f %10.6f''' axis = (0,0,1) import Matrix as m flip = m.rotation_from_axis_angle((1,0,0), 180) # 180 degree rotation about x. flip = [r + (0,) for r in flip] # Zero translation. for i in range(14): a = 360.0*i/7.0 t = m.rotation_from_axis_angle(axis, a) # Rotation by i/7 turn about z. t = [r + (0,) for r in t] # Zero translation. if i >= 7: t = m.multiply_matrices(flip, t) # Exchange top and bottom ring. print format % ((i,) + t[0] + (i,) + t[1] + (i,) + t[2])

1 0

obtaining rotation angles
by Jaap Brink 06 Oct '08

06 Oct '08

Hi, I'm trying to figure out how I can obtain angles from chimera. I have a 3D object that I have to rotate in order to see certain features. I'd like to know those angles. Is there is a way to get this info? Thanks in advance, Jaap Brink

4 4

Re: [Chimera-users] symmetric fitting
by skmolugu＠miners.utep.edu 06 Oct '08

06 Oct '08

HI, In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. thankyou, sudheer

3 2

Failure of Surface Display
by Charles Letner, Ph.D. 04 Oct '08

04 Oct '08

Hello, I am trying to display a surface using the Actions > Surface>Show menu. The surface is not displaying and the following error is in the reply: C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed (code 5). Falling back to single-component calculation. C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 I am using Chimera version: production version 1 build 2540 2008/07/09 Platform is Windows Vista 64 bit. The file I am working with contains 2 subunits. If I split the two subunits into separate files and open individually in the same session, the surfaces display without any issue. I am trying to show the surface of the two subunits associated, not the surface of each individual subunit. Any help will be appreciated. Cheers, Chuck

2 1

Re: [Chimera-users] Failure of Surface Display - Additional Info
by Charles Letner, Ph.D. 04 Oct '08

04 Oct '08

I just installed the latest daily build (1.2562) and get the same error. ----- Original Message ----- From: Charles Letner, Ph.D. To: chimera-users(a)cgl.ucsf.edu Sent: Saturday, October 04, 2008 11:59 AM Subject: Failure of Surface Display Hello, I am trying to display a surface using the Actions > Surface>Show menu. The surface is not displaying and the following error is in the reply: C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed (code 5). Falling back to single-component calculation. C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 I am using Chimera version: production version 1 build 2540 2008/07/09 Platform is Windows Vista 64 bit. The file I am working with contains 2 subunits. If I split the two subunits into separate files and open individually in the same session, the surfaces display without any issue. I am trying to show the surface of the two subunits associated, not the surface of each individual subunit. Any help will be appreciated. Cheers, Chuck

1 0

volume viewer question
by Ben Keshet 03 Oct '08

03 Oct '08

Hi Chimera fans, Can someone please help me understand how to read and look at .nrg files (generated by Grid)? I am interested in visually exploring the electrostatic potential around a protein. Specifically, when I opened it, everything was in one color, with negatively charged regions being darker, but I would imagine that positively charged regions should have a different color. On a related note - is there a tool to calculate and view the electric field lines around a molecule / protein? Thanks for your time and help, Ben

2 1

Poor performance with 30 molecules
by Thomas Goddard 03 Oct '08

03 Oct '08

Hi Ben, The main trick to improve efficiency in Chimera with many copies of a molecule is to use only the C-alpha coordinates. This is usually acceptable with working with EM data resolutions. You create a PDB file with only the CA atoms (can use "select @CA" command and Chimera File / Save PDB...) reducing the total number of atoms by 10x or more. Chimera is a very memory inefficient with molecules taking about 2 Kbytes per atom. This is about 10x worse than PyMol and VMD. You start feeling this at about 100,000 atoms and up and run into real trouble around 500,000 atoms if you are using 32-bit Chimera (no 64-bit available on Windows or Mac) because you run out of address space. The ability to rotate the models depends on rendering speed. Above 100,000 atoms only "wire" style will be fast and you must have a graphics driver installed (not Mesa on Linux). With a 4 year old graphics card (Radeon 9800 Pro) I get 10 frames per second with 200,000 atoms. With a newer card you should handle 500,000 atoms in wire at reasonable frame rates. Chimera session files include all the PDB atom coordinates. Chimera has no way to show 30 copies of a PDB file at different positions without having 30 independent copies of the data, except using surfaces with the multiscale tool. The multiscale tool does not interoperate easily with fitting in maps. Tom Elaine Meng wrote: > Begin forwarded message: > >> From: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> >> Date: October 2, 2008 10:24:34 AM PDT >> To: Elaine Meng <meng(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] volume viewer window >> >> Hi Elaine, >> I just aligned a tiny subtomogram to a model with a lot of different >> parameter, which generated many volumes. Then I wanted to visualize >> all the results at once. Since each volume was tiny, chimera was not >> struggling, it was fine :-) >> >> However that reminds me another issue about memory I had sometime ago. >> I have a tomogram into which I have fitted many copies (more than 30) >> of the same pdb file. There are two problems: 1) compiling the session >> file takes ages (around 10 minutes I would say). Opening the compiled >> session file takes more than 1 minute. >> 2) if I display all the copies of the pdb, everything is very slow (I >> mean if I want to move anything in space, it takes very long). If I >> display only a few copies (plus 1 or two slices through the tomogram), >> then it works fast. >> >> For the 2nd problem, there is maybe no easy solution to speed up the >> calcultations, but for the first one, since we are dealing with copies >> of a single pdb, wouldn't it be possible to make the process faster? I >> reckon that the coordinates of each atom of each copy of the pdb are >> saved. Would there be a way to save only one copy and transformation >> matrix for every copy? Would it speed up file saving-compiling-opening >> operations? >> >> Cheers, >> Ben > > Hi Ben, > I know Tom Goddard has made many recent improvements in Volume Viewer > memory usage and speed, but it sounds like your main issue is many > atomic structures rather than lots of volume data. > > If the PDB copies are identical except in transformation, there is some > capability in Multiscale Models to only store one copy of the > coordinates and show the others as low-res surfaces. However, as soon > as you try to show any more detailed display such as ribbons or atoms > and bonds, the full coordinates for that copy are loaded. If you > actually want to view ribbons/atoms/bonds for each copy, I don't know of > any mechanism to save memory. Also, to use Multiscale Models in this > way, you would have to generate an input PDB file with matrices > describing all of the transformations, which sounds difficult. Yet > another way to handle multiple coordinate sets for the same atoms is as > a trajectory. However, then you can only view one member of ensemble > (one "time step" from the trajectory) at a time, so that also would not > solve your problem. > > I CC'd Tom and Eric in case they have any ideas. > Best, > Elaine > >

4 3

Re: [Chimera-users] [Fwd: Re: [Dock-fans] DMS replacement]
by Elaine Meng 03 Oct '08

03 Oct '08

Hi Christian, We're glad you like the "Write DMS" tool in Chimera! <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/dms.html#writedms> Note that it does not run a surface calculation, but simply converts the molecular surface already shown in Chimera into the DMS format for output. Thus it effectively uses whatever parameters you had used to calculate the molecular surface in Chimera. That is currently done with MSMS (included with Chimera), a different program than DMS with different heuristics, so even with the most similar parameters possible I don't think the dots would be in exactly the same places even though the surfaces would basically coincide. More about molecular surfaces in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > If you used Chimera defaults for surface calculation, the probe radius is the same as the DMS default (1.4 Angstroms), but the atomic radii and dot density are different. The dms man page says the default density gives about 5 dots per square Angstrom. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html> You could set the Chimera molecular surface vertex density to 5 (instead of the default 2) to be similar to the dms default. To change an existing surface, Ctrl-click to select it and then for "MSMS surface" in the Selection Inspector (Actions... Select) change the "vertex density" value. If you want to change the Chimera defaults so that future surfaces will be created with that density, choose Favorites... Preferences, go to the "New Surfaces" category, change the value, click Save. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surf… > Default atomic radii in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I don't believe the old DMS default radii are necessarily better than the Chimera default atomic radii, but if you really wanted to set the radii in Chimera to these values, it can be done with the "Define Attribute" tool or the command "defattr" along with the attribute assignment file dmsrad.txt attached below (it is a very small, simple text file). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > I personally favor having Write DMS as a separate tool from Dock Prep because I think people should display the surface, adjust which part is displayed (since there is a nice option to only write what is displayed), and possibly change the surface calculation parameters rather than clicking a single button on Dock Prep to just do everything and write the whole surface without tailoring it to the situation. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > > From: Christian Schudoma <schudoma(a)mpimp-golm.mpg.de> > Date: October 2, 2008 5:48:57 AM PDT > To: "dock-fans(a)docking.org" <dock-fans(a)docking.org> > Subject: Re: [Dock-fans] DMS replacement > > I think WriteDMS is a very nice new feature for Chimera. Does it run > with the same default parameters as the original dms? > > Also, I wonder if it would be possible to integrate WriteDMS into the > DockPrep tool? Maybe add an option there to run surface generation and > WriteDMS automatically when DockPrepping a molecule? > > Thanks & best regards, > Christian >

1 0

Display symmetry axis
by Thomas Goddard 02 Oct '08

02 Oct '08

Katryna Cisek asks about display of symmetry axis: Hello Tom, Thank you for your suggestion, the code below is working very well for finding the symmetry information that I need for my dimers. Is it possible to visualize the axis of symmetry and the shift? I'm trying to reproduce a reference dimer conformation/symmetry using two monomers that have been docked to each other, but have not been able to get the exact symmetry numbers as for my reference structure, Thanks, Katryna On Fri, Sep 26, 2008 at 3:26 PM, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: > > Hi Katryna, > > > > To find a dimer symmetry axis I would open two copies of the PDB model. If > > the monomers are chain A and chain B then align chain A of one copy to chain > > B of another copy using the matchmaker command. Then print the rotation axis > > of the transformation between those two models. Unfortunately there is no > > command for this last step so I've attached a Python script that will print > > that information. > > > > Tom > > > > Example use: > > > > # > > # Report the transformation mapping one model to another, including axis of > > # rotation. Written to find dimer symmetry axes. Example: > > # > > # open 1f5w > > # open 1f5w > > # mmaker #0:.a #0:.b pairing ss > > # open symaxis.py > > # > > # Reply log output: > > # > > # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 > > # RMSD between 118 atom pairs is 0.337 angstroms > > # > > # Matrix rotation and translation > > # 0.69329933 -0.72016666 0.02638219 22.81733764 > > # -0.72021136 -0.69368986 -0.00948567 58.05835625 > > # 0.02513232 -0.01242434 -0.99960692 102.03253762 > > # Axis -0.92013562 0.39134963 -0.01399645 > > # Axis point 0.00000000 33.92575324 50.81758910 > > # Rotation angle (degrees) 179.90850597 > > # Shift along axis 0.29797742 > > # > > > > > > Katryna Cisek wrote: >> >> >> >> Hi, >> >> Is there a way of calculating symmetry for a dimer structure >> >> in chimera, e.g. axis of symmetry? >> >> Thanks, >> >> Katryna >> >> _______________________________________________ >> >> Chimera-users mailing list >> >> Chimera-users(a)cgl.ucsf.edu >> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > > > > # > > # Report the transformation mapping one model to another, including axis of > > # rotation. Written to find dimer symmetry axes. Example: > > # > > # open 1f5w > > # open 1f5w > > # mmaker #0:.a #0:.b pairing ss > > # open symaxis.py > > # > > # Reply log output: > > # > > # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 > > # RMSD between 118 atom pairs is 0.337 angstroms > > # > > # Matrix rotation and translation > > # 0.69329933 -0.72016666 0.02638219 22.81733764 > > # -0.72021136 -0.69368986 -0.00948567 58.05835625 > > # 0.02513232 -0.01242434 -0.99960692 102.03253762 > > # Axis -0.92013562 0.39134963 -0.01399645 > > # Axis point 0.00000000 33.92575324 50.81758910 > > # Rotation angle (degrees) 179.90850597 > > # Shift along axis 0.29797742 > > # > > from chimera import openModels > > from Matrix import xform_matrix > > from FitMap.gui import transformation_description > > from Accelerators.standard_accelerators import show_reply_log > > > > xf0, xf1 = [m.openState.xform for m in openModels.list()] > > xf = xf0.inverse() > > xf.multiply(xf1) > > tf = xform_matrix(xf) > > print transformation_description(tf) > > show_reply_log() > > > >

1 1

volume viewer window
by Benoit Zuber 02 Oct '08

02 Oct '08

Hi, In the pannel threshold and color in the volume viewer window, is there a way to switch between the displayed histograms? For example I have 33 volumes open, but I can only modify the threshold for the last 8 volumes that I opened, even if I set the maximum number of displayed thresholds to more than 8. Indeed then the window is not large enough to display all the thresholds. Thanks in advance, Ben -- Benoit Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK

3 3