- Chimera-users - RBVI Mailing Lists

Graphics Driver not switching to Nvidia
by a.pushpanath＠mail.cryst.bbk.ac.uk 22 Nov '13

22 Nov '13

Dear Chimera Users/Admins, I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! The intel HD graphics card is not good enough for my needs. Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera STL files
by Tom Goddard 20 Nov '13

20 Nov '13

Hi Julian, The problem is that you create a large density map for your protein, but then Chimera doesn't display it at full resolution, because it is so large. To make Chimera display the contour surface of the full resolution map set the "Step" value in the volume viewer dialog to 1, or use the equivalent command "volume #0 step 1" after the molmap command. Making the grid spacing 0.1 (40 times smaller than the resolution of 4 Angstroms) is likely to create a huge STL file that the printer will have trouble with, and it won't give any smoother appearance than say 0.4 I think. Tom On Nov 20, 2013, at 7:54 AM, Julian Gough wrote: > Dear Tom, > > I read what you wrote here: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008825.html > > I am really struggling to make an STL file for a coiled coil protein for 3D printing. What I see happening in Chimera does not seem to correspond to what you say, i.e. I use "molmap #0 4 grid 0.1" which according to you should be super-smooth -being far beyond what you suggest-, but the STL file that I export still has very large and obvious triangles. > > I have played with it a great deal and I cannot find any way to control the number of triangles in the STL file. Whatever parameter I use for the grid, the output file is roughly similar in size. I can certainly fill the memory and crash it by making the grid smaller, but this is not reflected in the exported STL file. > > ANy guidance much appreciated. > > Julian > > > -- > ~~~~~~~~~~~~~~~~ > Julian Gough > Professor of Bioinformatics > University of Bristol > Department of Computer Science > Merchant Venturers building > Woodland rd, Bristol, UK, BS8 1UB > Tel: +44 (0)117 3315221 > Web: http://bioinformatics.bris.ac.uk > <owen2.py><owen2.stl>

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Set interatomic distances
by George Patargias 18 Nov '13

18 Nov '13

Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)? Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

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measuring distances
by Ryan Pavlovicz 18 Nov '13

18 Nov '13

Hi, I am trying to measure the distance between two atoms from many different PDB structures using a python script. Using a command like: chimera.runCommand('distance #0:1@C1 #0:1@C2') will correctly output the distance within a tenth of an angstrom, however, i would like to output a more accurate measurement (more decimal places). Is there a way to do this when using chimera within a python script? Thanks for your help, ryan

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Commands for label formatting (font size etc)
by Andreas Göransson 18 Nov '13

18 Nov '13

Hi! How do I set font size for label / rlabel command in a command file? Can't find info in the documentation or in the mail list archive. Thanks, Andreas

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WebGL
by Hansen, Bryan (NIH/NIAID) [F] 18 Nov '13

18 Nov '13

Hi, I'm trying to export a scene using the WebGL feature within Chimera, but something seems to be going wrong. I'm attaching what opens up after Chimera saves the scene. I'm not able to rotate the output at all either. Is there a setting I need to change somewhere within Chimera? Thanks for your help and input. ************************** Bryan Hansen Microbiologist Electron Microscopy Lab NIH/NIAID/Rocky Mountain Laboratory 903 S 4th St Hamilton, MT 59840 (406) 363-9202 *********************************************************** 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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Changing default max number of histograms shown
by Joel Meyerson 18 Nov '13

18 Nov '13

Hi, By default, Chimera displays up to 3 histograms in the "Volume Viewer". I know that this number can be increased manually in the "Data display options" after launching the program, but I would like to change the default number. Is there a built-in Chimera preference to set the default number to something higher? If not, can you perhaps suggest how this might be scripted to happen upon launching the program? Thanks, Joel

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Multi-fragment fit in map
by Paolo Swuec 18 Nov '13

18 Nov '13

Good morning, I am EM user and I was wondering wether is possible in Chimera to fit multiple pdb in the same volume (e.g. Fitting two monomers into a dimer map without overlaps and clashes). I am using Situs and the collage command, but I was wondering if there was an easy way of doing it in Chimera. Thank you very much, Paolo Paolo Swuec, Ph.D. Student Architecture and Dynamics of Macromolecular Machines London Research Institute Clare Hall Laboratories Cancer Research UK South Mimms Herts EN6 3LD, UK E-mail: paolo.swuec(a)cancer.org.uk<mailto:alessandro.costa@cancer.org.uk> NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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Question on labeling residues on a single-chain protein
by J. David Puett 15 Nov '13

15 Nov '13

I wish to label certain residues and have these appear along with the structure. I have used the Command line to enter the following. rlabel Met_71.A What other Command(s) is required to display and later print the labeled structure? Many thanks!

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Measure buried area
by Jian Guan 15 Nov '13

15 Nov '13

Hi all, I use measure command to calculate the buried area between capsomer and Fab. My input file is pentamer.pdb and Fab.pdb. I made surface model for them respectively and use the command line as shown below: measure buriedArea #3 #2 probeRadius 1.4 However, it replied as "Surface calculation failed" I tried also delete all non-binding units in the pentamer, it still can not work. Does anyone know how to deal with that? Thank you so much. Sincerely yours, Jian

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