November 2006 - Chimera-users - RBVI Mailing Lists

question about using swapaa in Chimera
by Ng, David (NIH/NCI) [E] 22 Nov '06

22 Nov '06

Hi, I'm currently learning to use Chimera. I wish to look at specific amino acid mutations in CDKN2A for effects in conformational changes and changes in protein interactions with known partners. When I type the command "swapaa P #0:24" in chimera to mutate arginine 24 to proline in CDKN2A, I get an error message that says "Value error: No connectivity template for residue P" Can you help me with this issue? Thanks. David Ng, M.D. Staff Clinician

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Re: [Chimera-users] Get angles in degree out of Rotation matrix
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi Michael, It is not very common to specify a 3-dimensional rotation in terms of a x-axis rotation, y-axis rotation and z-axis rotation because this decomposition depends on the order of the x, y, and z rotations. If you rotate 90 degrees about the x-axis, then 90 about the y-axis you get a different orientation than if you do the y-axis rotation first followed by the x-axis rotation. Chimera has a routine to produce the rotation axis (a unit vector in 3-dimensions) and rotation angle about that vector corresponding to a 3x3 rotation matrix. You could use that in Chimera with some Python code. If you just want the rotation angle and don't need the axis then the formula is simple Tr(R) = 1 + 2*cos(theta) where Tr(R) = sum of rotation matrix diagonal elements so the rotation angle theta = arccos((Tr(R) - 1)/2) Below I give the Chimera C++ code that also computes the axis. There are corner cases handled by this code for 0 degree and 180 degree rotations. Tom void Xform::getRotation(Vector *axis, Real *angle) const { Real cosTheta = (rot[0][0] + rot[1][1] + rot[2][2] - 1) / 2; if (fuzzyEqual(cosTheta, 1)) { *angle = 0; (*axis)[0] = (*axis)[1] = 0; (*axis)[2] = 1; return; } if (!fuzzyEqual(cosTheta, -1)) { *angle = degrees(acos(cosTheta)); Real sinTheta = sqrt(1 - cosTheta * cosTheta); (*axis)[0] = (rot[2][1] - rot[1][2]) / 2 / sinTheta; (*axis)[1] = (rot[0][2] - rot[2][0]) / 2 / sinTheta; (*axis)[2] = (rot[1][0] - rot[0][1]) / 2 / sinTheta; return; } *angle = 180; if (rot[0][0] >= rot[1][1]) { if (rot[0][0] >= rot[2][2]) { // rot00 is maximal diagonal term (*axis)[0] = sqrt(rot[0][0] - rot[1][1] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[0]); (*axis)[1] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[0][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } else { if (rot[1][1] >= rot[2][2]) { // rot11 is maximal diagonal term (*axis)[1] = sqrt(rot[1][1] - rot[0][0] - rot[2][2] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[1]); (*axis)[0] = halfInverse * rot[0][1]; (*axis)[2] = halfInverse * rot[1][2]; } else { // rot22 is maximal diagonal term (*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1] + 1.0f) / 2; Real halfInverse = 1 / (2 * (*axis)[2]); (*axis)[0] = halfInverse * rot[0][2]; (*axis)[1] = halfInverse * rot[1][2]; } } }

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Re: [Chimera-users] suggestion
by Thomas Goddard 20 Nov '06

20 Nov '06

Hi David, Thanks for your suggestion to add coloring of isosurfaces based on gradient magnitude to Chimera. I think I can add this to the Surface Color tool in an hour or two since the gradient calculation code is already in Chimera (for fitting atomic models in maps). I'll try to put it in soon and send you the code to test. Description of coloring from article: "OpenDX (www.opendx.org) module MAKROVIS was implemented to create masks of different shapes and to analyze disorder in the reconstructions (Figure 1B). For this, isosurface rendering of a given voxel was colored as a function of the maximum density difference between the voxel and its neighbors." Tom > From: "David G. Morgan" <dmorgan(a)ucdavis.edu> > To: goddard(a)cgl.ucsf.edu > Subject: suggestion > Date: Thu, 16 Nov 2006 19:03:50 -0800 > > Tom, > > I have a suggestion for the developers "list of ideas to implement," if > you think there would be enough interest from users and that it is > something that chimera should do. I realize that you get lots of > suggestions, and that some of them are simply outside the realm of what > the chimera developers think chimera is intended to do. But since you > do ask for suggestions, here's my most recent one. > > I'm attaching a recent journal article where the authors used a color > coding scheme to display "order/disorder" regions of an EM > reconstruction. The images are in Fig 1 B and the rather sparse > description of the "algorithm" is a single sentence in the "Image > Processing 3D Reconstruction" section (p 1046). The idea of color > coding some estimate of the better defined regions of a density map is > very nice (and clever), and would be extremely helpful in lots of > situations (my plug for wanting you guys to implement something > similar...). > > The idea behind this is that for any given region of iso-surface, the > density gradient normal to that surface should be a reasonable measure > of how well defined the density is. In other words, a very steep > gradient (e.g., a fast transition between protein and solvent) means > very well defined density and a flat gradient means weakly defined > density (disordered regions, partial occupancy, etc.). The authors > don't do such a complicated calculation, but it seems that what they > implemented at least captures most of this sort of character. > > I think the key to this is that the gradient is calculated "locally." > I've looked at gradients as a function of resolution with the idea of > using it to help chose a proper iso-surface. While it works well with > model data, real reconstructions aren't nearly so well behaved. I > hadn't thought about this in a while, but I think what the authors have > done both helps explain the behavior of my real data (the gradient is > simply too varied) and is a quite useful visualization tool. > > So please think about implementing something like this in the volume > handling tools of chimera. > > David Gene Morgan > Advanced Microscopy & Proteomics > Molecular & Cellular Biology > University of California at Davis > 530 752 2693 (lab) > 530 752 3085 (FAX) > ---- > removed PDF for > > Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ. > Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. > Structure. 2006 Jun;14(6):1039-48.

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Duplicate Atom Serial Numbers
by Albion Baucom 17 Nov '06

17 Nov '06

When I generate a PDB file, and generate symmetry related biological units, I frequently replicate the single structure. When I do this the atoms numbers get duplicated and when I open the structure in Chimera it prints to the screen warning: duplicate atom serial number found: NNNN where NNNN is the duplicate number. The problem with this is it slows down opening the file by a huge factor. I assume that the print statement to the terminal is adding a lot of time to the file reading process. Is there any way around this, or a way to simply turn this off? I am not concerned with the specifics of the duplicate atom numbers. A single error message to alert me the fact that there are duplicate atoms would be enough. Once Chimera is done reading the structure it works fine. Rotations are smooth. Displaying ribbons is quick, etc. This doesn't appear to be a slow down due to atom limitations, but simply the overhead of printing that error message over and over to the console. Of course I am aware that there are BIOMT records to generate symmetry related molecules using a single repeating unit, or I could generate separate PDB files for each repeating unit, but this is a lot more work and bookkeeping when I can use some existing simple programs to simply rotate and translate a single set of coordinates. Thanks Albion

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deleting model memories
by wendy ochoa 15 Nov '06

15 Nov '06

Is there a way to delete model memories in the emanimator option? thanks a lot wendy

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Question about molecular surface generation
by Nihshanka Debroy 15 Nov '06

15 Nov '06

Hi Chimera users, I have been generating molecular surfaces for several proteins and am hoping to perform some matrix calculations on the points where the surfaces are being calculated. So I was wondering if there is a way to reduce the # points where the surface is calculated/plotted, as that would really reduce the dimensions of my matrices! I am using the Delphi Controller to generate electrostatic potentials. My understanding of Delphi is that it finds finite difference solutions to the Poisson Boltzmann equation by mapping the system onto a grid of points. After the potentials are calculated at those grid points, when generating the potentials on the molecular surface, interpolation is used to calculate the potentials for locations on the molecular surface that are between points on the grid used in Delphi. So I don't think its the grid size for Delphi that I need to be reducing, but the # points where the actual molecular surface is calculated. Is it possible to reduce this number somewhere in the code files? Thanks a lot! Sincerely, Nihshanka

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MultiAlign viewer
by Mireille Krier 14 Nov '06

14 Nov '06

Dear all, I want to add to the header of a sequence alignment graphical representations such as cylinders and thick arrows to symbolize stretches of helix and strand. Is this possible? Should one annotate this in the Stockholm format file (and if yes could you provide me an example file) ? Cheers, Mireille

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About electrostatic potentials
by xiaobinfan＠tju.edu.cn 14 Nov '06

14 Nov '06

Dear Sir/Madam: Thank you for reading. I am a new Chimera's user in China. I wonder whether the surface of a virus opened by Chimera could be colored by its electrostatic potentials calculated by the DelPhiController. I can color the surface of a small protein on Linux platform now. However, the surface of a whole virus (PDB 1ny7) opened by the Multiscale Models could not. Does it possible to do that? Thank you for your support. Best wishes! Sincerely, Xiaobin Fan ---------------------------

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Fwd: longbond and session restore problems
by Elaine Meng 14 Nov '06

14 Nov '06

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: November 14, 2006 10:36:35 AM PST > To: jean-francois menetret <menetret(a)bu.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu>, Thomas Goddard > <goddard(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] longbond and session restore problems > > Hi Jean-Francois, > In my tests I didn't have this problem; showing Pipes-and-Planks > should not change which atoms and bonds are shown. > > However, I might understand what is happening: when you show the > "chain trace" of CA atoms only, a connection across the missing > part is shown even after you use "~longbond". This CA connection > line is different than the "missing segments" pseudobonds: > > -CA-CA-------CA-CA- > is the chain trace, not affected by ~longbond > > -N-CA-C- - - -N-CA-C- > is the backbone showing "real bonds" except for the pseudobond, > which is affected by ~longbond > > If you are showing just the CA atoms and you don't want the > connection, here are some possibilities: > (1) just hide all the CA atoms (for example, command: ~disp @ca) > OR > (2) change from "chain trace" (the CA atoms) to "backbone > only" (N,CA,C) - if you used ~longbond the connection will be gone > OR > (3) if you really wanted to keep showing just the CA atoms, you can > select each long CA-CA bond (which is also a pseudobond, although > not shown with a dashed line) with Ctrl-click, and use the > Selection Inspector to undisplay it. This tool is opened by > clicking the button on the lower right of the Chimera window. In > the Inspector, change to Inspect [Pseudobond] and change the > "displayed" attribute to "false." > > I hope this helps, > Elaine > > On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote: > >> Hi Elaine, >> >> thank you for your message >> I still have one problem with the long bonds, though : there >> reappear in pipes-and-plancks. >> About restoring a session, I agree, it was not an issue with the >> chimera version but with the speed/memory of my PC. Although >> chimera could save the session, it couldn't reopen it on my PC but >> it did on a faster one. >> >> Best wishes >> >> Jean-François Ménétret, PhD >> Boston University School of Medicine >> Physiology and Biophysics Department >> 700 Albany Street W315 >> Boston, MA 02118 >> Email: menetret(a)bu.edu >> Mailing address: 715 Albany Street > > ----- > 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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longbond and session restore problems
by Thomas Goddard 09 Nov '06

09 Nov '06

Here are two problems reported by Jean-Francois Menetret in Chimera 2304 and 2306. ------- Start of forwarded message ------- Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST) From: jean-francois menetret <menetret(a)bu.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: problems report Hi Thomas, I have two problems to report 1) the longbond command doesn't seem to work (with chimera 2304 or 2306) 2) I saved a session under chimera 2304 but couldn't open it after=20 upgrading to 2306 Jean-Francois Jean-Fran=E7ois M=E9n=E9tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street ------- End of forwarded message -------

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Chimera-users November 2006