- Chimera-users - RBVI Mailing Lists

how to find
by Bishwajit Das 18 Feb '12

18 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* * --

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bug report
by Longfei Wang 16 Feb '12

16 Feb '12

Hi there, For nogui Chimera: Calls with script in nogui mode create the following traceback. terry@daisy[14]% chimera --nogui --script "coord_for_cluster_ATP_ bothChiFlip.py" Traceback (most recent call last): File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimeraInit.py", line 618, in init chimera.initializeGraphics() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/__init__.py", line 2114, in initializeGraphics bgprefs.initialize() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 211, in initialize onDisplay=_bgPrefDisp, onHide=_bgPrefHide) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 567, in register self._loadCategory(category, cat, inherit, convert) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 482, in _loadCategory cat.load(self._loadDict[name]) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 249, in load opt.set(value, asSaved=True, fromPref=True) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 64, in set self._callback(self) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 53, in _backgroundColorCB Midas.background(color=color, setMethod=False) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/Midas/__init__.py", line 966, in background method = chimera.viewer.Solid AttributeError: '_chimera.NoGuiViewer' object has no attribute 'Solid' Best Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115

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Re: [Chimera-users] radius of gyration
by Eric Pettersen 15 Feb '12

15 Feb '12

On Feb 14, 2012, at 6:07 PM, Daniel Gurnon wrote: > Hi Eric, > The radius of gyration interest stems from a little project I'm > starting with an undergrad. I'm interested in the radius of gyration > because I'm curious about how accurate our pictures of biomolecules > are, at least the ones that come from crystal structures. I'd like > to compare predictions of size-related behavior derived from the pdb > with measurements of size in solution, using gel filtration, SAXS, > or light scattering. That said, I don't know if I want center of > geometry or principal axis! Any advice? Hi Dan, I'm no expert, but it sounds like you want the radius of gyration from the center of geometry. Nonetheless, I'm cc'ing this to the chimera-users in case any others have thoughts. In an old posting to chimera-users, Elaine Meng provided a Fortran program to compute the radius of gyration: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003648.html I've attached a Python script that will print the center of geometry and radius of gyration from that center in Chimera's reply log. Run the script simply by opening it with File->Open. Depending on whether you feel nearby waters and ions will contribute to the measurements you are trying to model, you may or may not want to delete water and ions before running the script. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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radius of gyration
by Daniel Gurnon 14 Feb '12

14 Feb '12

Hi all, Can Chimera determine (or has a script been written to determine) the radius of gyration for a pdb structure? Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] possible Chimera bug?
by Ofeliia Mada 14 Feb '12

14 Feb '12

TkkyuluR X,=)RSISXSN:-P:(:=(=(=(=(=(:O(, G Sent from my Windows Phone esdcqppwevemeem

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fly command
by rswett＠chem.wayne.edu 14 Feb '12

14 Feb '12

Is anyone else having issues with the fly command lately? Seems like since RC 1.5ish flying to a savepos ignores the # of frames it's set to fly over. i.e. fly 50 in (where in is a saved position) does the fly in one frame, appearing the same as fly in or fly 1 in Additionally fly in 50 has the same effect. Has anyone else run into this? I have a few saved sessions i'd like to animate, and the older versions are having none of it. Suggestions? ~Rebecca

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Re: [Chimera-users] meaning of the ANISOU PDB parameters
by Eric Pettersen 13 Feb '12

13 Feb '12

On Feb 10, 2012, at 1:55 PM, Julian Chen wrote: > hi Eric, > > First of all, hello, I was in Stroud's lab for many years, until > 2003, when I left SF. Hi Julien! > I am in a rather interesting situation where we have been dealing > with neutron and X-ray refinement, and we have been able to do > anisotropic refinement on selected hydrogen atoms, from having high > resolution neutron data. I've been using Chimera. > > I am still somewhat confused as to the meaning of the six ANISOU > terms, I understand that the first three describe the three > orthogonal axes of the ellipsoid, and that the last three somehow > relate this to the coordinate space. The six terms actually describe a 3x3 matrix that is symmetric about the diagonal. The eigenvectors and eigenvalues of that matrix are the atomic displacement axes and the mean squares of the displacements respectively. The first thing to know is that the values shown in the ANISOU records are scaled by 10**4. The other thing to know is that the six numbers correspond to these positions in the matrix: 1,1 2,2 3,3 1,2 1,3 2,3. Since the eigenvalues are mean squares, one typically works with the square roots of the eigenvalues. > Specifically, I want to look at the ANISOU for the H/D atoms, and > want to try to correlate it to its bonded neighbor (the C or the N > or the O). If possible, I'd like to extract some vector for the > 'directionality' of the aniso atoms and relate them to one another. > I want to see if the vibrational motions of the hydrogen are > correlated to the vibrational motions of its bonded neighbor. Is > there anything in CHIMERA that could do something like this, or some > appropriate mathematical formula that could output the right sort of > information? The ellipsoids option in the program gives a > qualitative description, but I'd like to get something a bit more > quantitative in nature. Depending on how comfortable you are with programming in Python, you could either write your own external code based on the info above, or write something that runs in Chimera. The latter does have the advantage of you not having to write PDB-parsing code an so on. In Chimera, atoms with corresponding ANISOU records have an 'anisoU' attribute which is a 3x3 matrix (the matrix is often referred to as 'U' in the literature, hence ANISOU record). This code snippet (basically copied from the Chimera's Aniso module) will extract the eigenvectors/values for an atom and take the root of the values: from numpy.linalg import svd ignore, lengths, axes = svd(atom.anisoU) from numpy import sqrt lengths2 = sqrt(lengths) Let me know if you need more info or help with scripting. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualising AutoLigand affinity points
by George Tzotzos 09 Feb '12

09 Feb '12

Hi, I'm attaching a jpg image of ligand affinity map fill points generated by AutoLigand. My question is whether there's a way to depict these fill points as "disconnected" spheres. Actions/spheres generates something like I'd like to see but the size of the spheres is too large. Regards George

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pi-cation interaction
by Bishwajit Das 09 Feb '12

09 Feb '12

how to find cation pi-interaction in a docked molecule.......plz help me -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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How to select
by Bishwajit Das 09 Feb '12

09 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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