April 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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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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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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depth cue by color for tomogram
by Michael Elbaum 18 May '15

18 May '15

Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138

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chimera meeting tomorrow
by Greg Couch 29 Apr '15

29 Apr '15

The agenda is available in advance! Thank you Conrad! Conrad says "feel free to add items" :-) https://plato.cgl.ucsf.edu/trac/chimera2/wiki/2015-4-30

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Auto dock Vina Increasing Exhaustiveness
by Tunc Morova 29 Apr '15

29 Apr '15

Hello! I am using UCSF Chimera, Autodock Vina extension for obtaining conformations of my protein and ligand. In this interface, As you know, I can change the exhaustiveness value between 1-8. However, since my system is more than 30x30x30 A, I need to get my exhaustiveness value more than 8 for getting more accurate results. But I can’t make it more than 8 through Auto dock Vina interface in Chimera. How can I increase this exhaustiveness value ? Btw, Instead of using Opal web service, I am using vina locally. Thank you many times for your help Best Regards Tunc Morova

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Converting sdf file into mol2 format
by Mahendra B Thapa 29 Apr '15

29 Apr '15

Dear Chimera users, I am trying to convert sdf file ( downloaded from* diversity set* data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html), I got the following error messages: Cannot find consistent set of bond orders for ring system containing atom #0.73:1@N1 --- Unknown redo atom type: N3 Traceback (most recent call last): Any suggestions for correcting these errors will be a good help for me. Thank you, Mahendra Thapa University of Cincinnati,OH

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Create an artificial bond between ribbons for 3D printing
by David Bhella 28 Apr '15

28 Apr '15

Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long. The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Chimera-users April 2015