September 2016 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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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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Chimera crashes on Mac OS Sierra (10.12)
by Tom Goddard 20 Oct '16

20 Oct '16

The Chimera developers have received 8 Chimera crash reports on the new Mac OS Sierra (10.12) somehow related to scrollbars. You may want to hold off updating to Sierra if you make heavy use of Chimera. We have not yet been able to reproduce the crash. It is very likely a bug in the Mac Tk window toolkit that Chimera uses, so even when we figure out how to reproduce it it may take time to figure out a fix since the problem is not in our code. Tom

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build a homotetramer based on crystallographic symmetry
by Shuanghong Huo 30 Sep '16

30 Sep '16

Dear All, Can UCSF Chimera build a homotetramer from a dimer based on crystallographic symmetry? Thanks, Sharon Huo Clark University

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3D to 2D
by Sameer K Singh 30 Sep '16

30 Sep '16

Hi, I was wondering if it's possible to extract information from 3D plots in Chimera and render them as 2d plots.Specifically I'm trying to extract information from a .bild file displayed in chimera and display it as a 2D plot of some kind in an external program (eg: excel) Thank you very much. Best, Sameer ________________ Sameer Singh, PhD Albert Einstein College of Medicine 1300 Morris Park Avenue New York, NY - 10461 Phone: 718-430-2048 Cell: 917-848-9319

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differentiating lower and upper case chain ID's
by Melissa Jurica 29 Sep '16

29 Sep '16

Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa

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Surface area list
by esserlo＠helix.nih.gov 28 Sep '16

28 Sep '16

Hi, with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand. Thanks for any advice. Lothar

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Problem with running Chimera
by Patty Tran 27 Sep '16

27 Sep '16

Hello! I installed two versions of Chimera (Microsoft Windows 64-bit chimera-1.11.2-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> and Microsoft Windows 64-bit chimera-1.11-win64.exe) <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> I have only been able to run the program once and that was when I clicked "start program" after installing the 1.11 version. I have been unable to find the Chimera desktop icons and the program itself in the list of programs. I thought I could find the programs under my C:/Program Files/Chimera but there are no folders. Could someone provide instruction on how to uninstall the programs and install them so I could find and use the program easily? Thank you. Patricia

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Measuring angles and distances between planes defined by two aromatic rings
by George Tzotzos 26 Sep '16

26 Sep '16

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions. I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution). Thanks in advance George

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Interpolate colors in Morph after Color zone
by Haselbach, David 26 Sep '16

26 Sep '16

Hi everyone, Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don't really like the edge that is created by the segmentation. Kind regards David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302

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Chimera-users September 2016