- Chimera-users - RBVI Mailing Lists

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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