November 2013 - Chimera-users - RBVI Mailing Lists

Problems with binding site representation
by vigneshwari subramanian 08 Nov '13

08 Nov '13

Dear all, I have been trying hard to make a figure similar to the one shown in this web page. http://www.cgl.ucsf.edu/chimera/ImageGallery/ I would like to have 2 different colours to represent the inner and outer surfaces of binding site. I opened 2 different structures of the same protein and adjusted the surface parameters (probe radius and vertex density) . But that doesn't seem to work. I would be really happy if someone can help me to sort out this issue. thanks, vigneshwari

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Group cylinder with a PDB and fit together
by Mario Dejung 07 Nov '13

07 Nov '13

Hi all, I created a some cylinders in chimera to visualise the symmetry axis and the rotation center of a hexametric structure. Is there a way to fix the position of these cylinders relative to the pdb structure? So when I fit the structure, the cylinders will also rotate in the same way. And, by the way, is it possible to duplicate these cylinders, or do I have to create a .bild file and import it several times? Thanks for your feedback. Mario

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How to change the default color for pseudobonds?
by Oliver Clarke 06 Nov '13

06 Nov '13

Greetings, Is there any way to change the default color for pseudo bonds (e.g. distance monitors)? I generally work on a white background, and the default of yellow is very difficult to see. Pretty much everything else in the Chimera GUI seems to be customizable, which I love, but I can’t see how to alter the default in this particular instance. Many thanks, Oliver.

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Specifc silouhettes
by m.maletta＠nki.nl 05 Nov '13

05 Nov '13

Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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chimera scalability on irix
by tyrrell t 04 Nov '13

04 Nov '13

I couldn't find any information on the subject, and have no hardware to test at the moment, but for a future deployment I need to work with IRIX systems, and I was wondering if chimera is coded to take advantage of multiple MIPS CPUs, or is it strictly a CPU-bound application? ie: would it run better on a dual-cpu octane system at 600mhz, or a 700mhz uni-processor fuel system? ( or something along this line )

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calculate axes from centroids
by Elaine Meng 04 Nov '13

04 Nov '13

On Nov 3, 2013, at 7:49 PM, Lili Peng <lilipeng(a)gmail.com> wrote: > Hi Elaine, > I've inquired you in the past regarding defining angles and planes in UCSF Chimera. > Do you know if there's a way to define an axis through two centroids, or through the center-of-mass of a residue and the centroid of a subunit, some combination like that? > Thank you, > Lili > Hi Lili, Currently, axes (and planes and centroids) can only be calculated from sets of atoms, not centroids. However, it can done in current Chimera by defining centroids, adding fake atoms at their positions, and using those atoms to define axes. You can specify whether each centroid calculation is mass-weighted (center of mass) or not (default, center of geometry). (a) use Axes/Planes/Centroids (or command "define") to define the desired centroids (b) look in Reply Log for the coordinates of each centroid ( c) add atoms: Tools… Structure Editing… Build Structure, Start Structure section, use settings to add atom with specific x,y,z coordinates to the existing model (the one whose atoms you used to define centroid) (d) use new atoms to define axis <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> There is also a "measure center" command that will automatically create a fake atom (option "mark true"), so you could use that instead for steps a-c, but it always does mass-weighting. For non-mass-weighted centroids, you would need to use the full process outlined above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> I hope this helps. Sorry it is not as simple as it should be. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera-users November 2013