- 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])

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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

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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

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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

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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

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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

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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 > >

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Re: [Chimera-users] [Fwd: Re: [Dock-fans] DMS replacement]
by Elaine Meng 02 Oct '08

02 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 >

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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() > > > >

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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

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cannot interpolate models: underlying C++ Atom object is missing
by Frembgen Kesner, Tamara A 01 Oct '08

01 Oct '08

Hello, Does anyone know what the error message cannot interpolate models: underlying C++ Atom object is missing means? (And what I can do about it?) I am getting this message when I attempt to create a morph between two .pdb files using minimize. Thank you.

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Re: [Chimera-users] 1HLA- how to make ribbon image?
by Elaine Meng 30 Sep '08

30 Sep '08

Hi David, To summarize for the chimera-users list: 1HLA is an alpha-carbon-only structure, which cannot be shown as a ribbon in Chimera. However, there are many other structures of this protein, several at higher resolution and including all backbone atoms, allowing them to be displayed as ribbons. This Uniprot page has a long list of structures (about 80% of the way down is a "3d structure databases" section): http://www.uniprot.org/uniprot/P01892 The best resolution looks like 1.4 Angstroms, structures 1i4f and 1oga. Both match up with the CA-trace in 1hla quite well. Since they include all backbone atoms, they can be displayed as ribbons. I suggest using 1i4f. 1oga is just as good but has two copies. I hope this helps, 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

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1HLA- how to make ribbon image?
by Edelshtein, David 30 Sep '08

30 Sep '08

Hello, I am an ITL researcher, I use chimera for making a ribbon image of 1HLA molecule, and I need to mark specific residues, (by the number/position). So far, I am unsuccessful in converting wire style to the ribbon style. Please let me know if you can help, advice or direct me to required info. David, Edelshtein SRA II UCSF ITL

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COLOURING A SUBUNIT
by Tom Goddard 30 Sep '08

30 Sep '08

skmolugu(a)miners.utep.edu wrote: > Hi, > thank you very much for your reply, > I have another question, is there a way to colour a symmetric map which has 4 subunits in to four different colours? > thank you for your time, > regards, > sudheer. > Hi Sudheer, If you have 4 monomer PDB models fit into the map, color them differently (e.g. command "rainbow chain"), then use the Color Zone tool to color the map to match the monomers. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorz… The Chimera volume guide may help with future questions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html Tom

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Re: [Chimera-users] SEPARATING A SUBUNIT
by skmolugu＠miners.utep.edu 29 Sep '08

29 Sep '08

Hi, I have a CryoEM density map with 14 subunits with seven fold symmetry. Is there a way in chimera to separate only one subunit from the entire map. thanks, sudheer

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Calculating RMSD for ligand
by 吴超 27 Sep '08

27 Sep '08

Hi, dear folks, I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command: rmsd #0:1.het & ~element.H #1:1.het & ~element.H But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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error in vista
by Mugnaioli, Enrico 25 Sep '08

25 Sep '08

Dear Chimera Users, I installed Chimera in my new PC, working under Vista. Apparently, the installation was fine, but when I started the program I got this error. What can I do? Best regards, Enrico Mugnaioli

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adding H
by Barbara Truitt 25 Sep '08

25 Sep '08

I have a compound which has an imidazole ring. When I Add Hydrogens, no hydrogens are added to the nitrogen atoms when I use the build from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of the charge assignments in the resulting mol2 file don't make sense. Barb Truitt

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Re: [Chimera-users] Creating and visualizing a plane
by Elaine Meng 24 Sep '08

24 Sep '08

On Sep 24, 2008, at 12:29 PM, Monica Tello wrote: > I found this very useful, thanks! > I have been trying to do a similar thing but creating a sphere to > put it surrounding the residues in the active site. I tried to > create a big water molecule, and this made the trick until I was > stuck because I can't change its transparency. Then I thought about > creating a marker such as you described for the plane, but I am not > familiar with creating these marker files and I am probably missing > commands in the .cmm file, because Chimera can't open the file and > is giving an error with the info written in it. > Could you help me out with it? Hi Monica, A marker is really just an atom, so that wouldn't make a difference. Normally you would use "Volume Tracer" (under Tools... Volume Data) to create the marker interactively with the mouse and then save it as a file from that tool instead of creating the file with a text-editor. I only edited the file in my example so I could specify the coordinates exactly. In fact, I created 3 markers interactively, saved the marker file from Volume Tracer, and then just edited the x,y,z coordinate values. You can make an atom/marker transparent by creating a transparent color and then using it (for example, choosing Tools... Utilities... Color Editor, clicking Opacity to include a transparency slider, creating the color, and using "colorpanel" as the color name in a command or "Actions... Color... from editor" in the menu). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html> You can also create and name transparent colors with the "colordef" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html> Show the atom in the sphere representation; you can change its radius, for example by selecting the atom and using a command something like: vdwdef 5.0 sel <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> In fact, the "Volume Eraser" tool (under Tools... Volume Data) just makes a big transparent marker and its dialog has convenient controls for changing its color, radius, and position, so you might want to try that instead: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase… > Yet another possibility is to make a spherical surface instead of an atom/marker. This can be done with the command "shape": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> You can move that spherical surface relative to your structure and change its color just as described for the planar surface in my earlier message to Jim. I hope this helps, Elaine ----- 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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Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data.
by Andy LiWang 24 Sep '08

24 Sep '08

Dear Chimera, I just installed Chimera on my Dell XPS 1210 laptop (Windows Vista; Mobile Intel(R) 945GM Express Chipset Family). I get the following error everytime I start Chimera: Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data. Molecules are not properly rendered and does not hide objects rotated behind other objects. I.e., some object appear in front regardless of rotation. This is a new problem. Chimera used to work fine on this computer. However, recently, I had Windows Vista reinstalled. Since the reinstallation, Chimera has these new problems. Any ideas? Thanks, Andy -- Associate Professor School of Natural Sciences UC Merced Atwater, CA 95301 Tel: (209) 228-4617 Fax: (209) 724-4356

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Re: [Chimera-users] Generating random helix
by skmolugu＠miners.utep.edu 24 Sep '08

24 Sep '08

Dear Chimera team, Is there any option in chimera that builds helix in a map at a position that is assumed to be a helix. thanks, sudheer

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Out of topic for Elaine
by Francesco Pietra 24 Sep '08

24 Sep '08

Hi Elaine: Although out of topic, as the author of the program "grid" you could be in the best position to give me general advice. Selecting spheres for only a portion of the protein failed to execute "grid" (at 0.3A grid_spacing) in a reasonable time. I choose this route in the hope to be able to examine docking (DOCK6) for the various parts of the molecule, in order to have the whole. I believe to have good reasons to do that. Is that what one should expect or does it mean that I did something wrongly? Thanks francesco pietra

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Movie recording
by Ibrahim Moustafa 24 Sep '08

24 Sep '08

Dear Chimera team, I have a problem with making a movie of morphed conformations in chimera (only for chimera 1.2548 installed on my laptop running XP). After doing the ³morph² when trying to record the movie I got the following error message: ³Error stopping/encoding movie: MidasError: Keyword and¹ does not match any known keywords² I don¹t understand the error message and what does it mean by ³keyword and²? I¹m not running a script. I don¹t have this problem with the Mac version of Chimera. The funny thing is that I was able to create a movie on the windows version a week ago. I¹m not sure if this problem has relation with XP and perhaps some new updates! Any idea how to solve this problem? many thanks for your great help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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