August 2008 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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using EMAN/AIRS/SSEHunter
by Peter Hildebrand 10 Dec '08

10 Dec '08

Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: <function command at 0x89f67d4> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter

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Models or chain
by hsosa＠aecom.yu.edu 09 Sep '08

09 Sep '08

I have created a model from several PDB files and saved it using the save PDB utility in chimera. The resulting PDB file had the different molecules separated in the PDB file with the lines MODEL 1 . . . MODEL 2 . . . MODEL 3 . . . and so on. Is it possible instead to save the PDB file as one model but using different chain names for the different molecules ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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v. 2540 linux - core dump (?!?!?!)
by Boaz Shaanan 03 Sep '08

03 Sep '08

Hi, After installing v. 2540 for linux I get 'floating exception' and core dump. The installation went fine as far as I can tell. It's a laptop running Mandrake 10. So far, I've had no problem running chimera on it. any clue about what might have gone wrong ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Chimera running un der 64 bit Vista
by Charles Letner, Ph.D. 03 Sep '08

03 Sep '08

Hello all, Does Chimera run under 64 bit Vista? Thinking about a new desktop and sure would like to go 64 bit. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004

2 1

assignment of charges
by Barb Truitt 02 Sep '08

02 Sep '08

I have two different pdb files that differ only in how the atoms are listed in the atom name columns. In one file all of the Carbon atoms are listed simply as C. In the other file, the carbon atoms are numbered C1, C2, etc. This is true for the other atoms in the molecule, which is not a peptide chain. The mol2 files created by Chimera under the dock prep procedure have different charges assigned to the atoms, differing most in the aromatic carbons. Some of the hydrogens also have different charges assigned to them. Most of the differences are small, but some are 10%. What is the explanation for this? Barb Truitt

2 1

sulfone
by Barb Truitt 02 Sep '08

02 Sep '08

I am trying to assign charges to a compound that contains a sulfone group. The charge assignment depends upon how I name the atoms. The atom assignment for the oxygens that are part of the sulfone group and the sulfur itself vary depending upon how they are named. How should I name them so that they are handled correctly? Barb Truitt PS - I receive the Chimera list emails, but my outgoing email address apparently doesn't match the one that I used to sign up for the list. Is there a way to fix that?

2 1

POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Help! I am having trouble saving my images when they have a surface clipped to show the inside. I attach an example for clarity, where the same view was saved with/without POV ray.. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica SURFACE CLIPPED WITH POV-RAY, SURFACE DOES NOT SHOW THE CLIPPING! ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Dear all, I am trying to save a Figure that shows my ligand with its surface around partly clipped, and use POV Ray. The problem is that POV Ray modifies the output of the figure: the final picture shows the full surface around the ligand, although on the screen I designed it so that you can see the surface partially clipped. If I use transparency on the surface, POV Ray also ignores this and shows still the full surface around the ligand, and opaque. If I don´t use POV Ray, then I get the figure as seen on the screen! Why is POV Ray ignoring the surface as I want it? It ignores any kind of alteration of the surface! I was using the default POX Ray settings, although by now I have tried to change some of the ones I thought may be related to this, based on the Chimera Manual, but I haven´t had any success. Can anyone help me with this? It will be very much appreciated! I include an example of the same figure saved with and without using POV Ray. The one without using POV ray is the one that looks like what I designed on the screen. Thank you very much!! Monica ----------- ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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Chimera-users August 2008