- Chimera-users - RBVI Mailing Lists

changing the rgb for stereo images
by Bala subramanian 13 Dec '13

13 Dec '13

Friends, I have a glass with a red-cyan color. When i use the Chimera stereo mode (red-cyan) under view controls. I still see some ghost images. I would like to know if there is any possibility to add a features something like a box where i can give the rgb (the light frequencies) values of the images to match my glass. Thank you, Bala -- C. Balasubramanian

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Dynamic scolor custom cmap?
by Hurt, Darrell (NIH/NIAID) [E] 13 Dec '13

13 Dec '13

Hi Chimera friends, I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): scolor #0 volume #1 offset 1.4 cmap cyanmaroon My problem become if I want to set a custom palette: scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green This line also works, but for values lower or higher than –10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from –29 to +17. Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? I'm happy to clarify if needed. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Modeling with cryo-EM
by Aurore Vaitinadapoule 13 Dec '13

13 Dec '13

Dear all, I'm would like tu use this following script to model with cryo-EM: from modeller import * log.verbose() env = environ() struct='./M60_9.pdb' map='new_map.mrc' resolution=10.2 box_size=48 # how to define the box size ?? apix=1.88 x=90; y=63; z=23 #origin steps=20 # Read in cryo-EM density map den = density(env, file=map, em_density_format='MRC', voxel_size=apix, resolution=resolution, em_map_size=box_size, density_type='GAUSS', px=x,py=y,pz=z) # Fit the PDB file into the map by MC simulated annealing den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='CENTER', number_of_steps=steps, angular_step_size=30., temperature=100., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log') But i got this error message: _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36) What is exactly the box size? And how to define it? Thank's Aurore -- Aurore G. VAÏTINADAPOULÉ aurore <a.vaitinadapoule(a)inserm.fr>.vaitinadapoule(a)inserm.fr<a.vaitinadapoule(a)inserm.fr> a.vaitinadapoule(a)gmail.com PhD Student in Bioinformatics INSERM UMR-S665, DSIMB Team, Dynamique des Structures et des Interactions des Macromolécules Biologiques Mobile phone: +33(0) 778 18 52 07

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chimera slow
by Daniel Murin 12 Dec '13

12 Dec '13

Hi, I have been trying to use the Unit Cell function on Chimera. It works, but the graphic is so large that moving it around is nearly impossible because the program is running so slowly. It is rendered in ribbon. Is there a way to lower the quality in order to manipulate the graphic faster? Thanks! Charles Daniel Murin Ph.D. Candidate - Ward/Ollmann Saphire Labs Integrative Structural and Computational Biology Immunology and Microbial Science Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CimBio 105 La Jolla, CA 92037 Office: 858.784.3326 Lab: 858.784.7170 Fax: 858.784.8218 email: cmurin(a)scripps.edu

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(no subject)
by Danilo Di Maio 12 Dec '13

12 Dec '13

danilo.dimaio(a)gmail.com

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Launch external program from Chimera python script?
by Hurt, Darrell (NIH/NIAID) [E] 11 Dec '13

11 Dec '13

Hi Chimera friends, I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": http://code.google.com/p/pymlp/ I see two ways to do this: (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Journal of Organic and Biomolecular Simulations: Full page charge waiver
by CompChem News 11 Dec '13

11 Dec '13

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select all side chains
by Zhou, Ming (NIH/NCI) [C] 09 Dec '13

09 Dec '13

Dear Elaine: I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? Thanks Ming Zhou

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Silhouette toggle
by Luca Pellegrini 06 Dec '13

06 Dec '13

Hi, I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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calculate buried surface area
by Bala subramanian 05 Dec '13

05 Dec '13

Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian

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