May 2018 - Chimera-users - RBVI Mailing Lists

Surface mesh and coloring queries
by Bala subramanian 29 May '18

29 May '18

Dear Chimera friends, Good day. Please enlighten on the following queries, a) I would like to know if I can write the surface mesh calculated within chimera to a file. From the documentation of the surface command, it seems that it is not possible. My idea is to have the vertices and faces as outputs to be fed to a plotting tool aimed for webpage display. Please guide me if this is possible or the related source code I can modify to have the output. b) How does chimera color surfaces, for instance, coulombic surface. What I am not understanding is the way the surface colors are interpolated to atomic charges. I would like to adopt the method for my plotting purpose. Thanks in advance, Bala -- C. Balasubramanian

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display vectors
by Michał Kadlof 24 May '18

24 May '18

Hi, I'm running MD simulation and I would like to display forces vectors "live". My strategy is to run: MD Movie -> PerFrame Script -> In this script create a shape (cone), and update it every frame. I transformed my vectors into ration axis and angle, and run it. However it works extreamly slow, and even lowering quality of cone didn't help. Do you have any clues? Here is how my script looks like: #1: close #1; shape cone radius 0.2 height 3.051701874476991 center :47 divisions 10 color red rotation 1.003198923120698,-0.8433298543660601,-0.5373867542336597,180 #2: close #1; shape cone radius 0.2 height 3.054021942152826 center :47 divisions 10 color red rotation 1.0022878678774028,-0.8433406134841704,-0.5373745205242975,180 #3 ... -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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coot/chimera model-map misalignment
by Gabriel Brandt 23 May '18

23 May '18

Hi. I've always been able to work around this problem, but I do often have to work around it, so I was wondering whether there's an easier way. Let's say I open a PDB file in Coot and export the map that it generates from the mtz file. If I attempt to open this ccp4-formatted map in Chimera, the coordinates appear to transformed so that the model and map are wildly misaligned in space. Normally, I work around this problem by using the map-generating feature in Phenix, which generates a model and map that align in Chimera. However, in this case, I'm trying to compare the maps that Coot generates on the fly to the those produced by Phenix, so it would be nice to be able to export a map from Coot and open it in Chimera. Thanks very much. gsb ………………………………... Gabriel Brandt Assistant Professor Department of Chemistry Franklin & Marshall College PO Box 3003 Lancaster, PA 17604 ph: 717.358.4846 shipping address: 415 Harrisburg Ave Lancaster, PA 17603 ………………………………...

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volume viewer ranges
by Tamas Hegedus 22 May '18

22 May '18

Hi, I have a .map file. If I open it in chimera, volume viewer indicates a range (-0.133 - 0.235 Level: 0.018 (in a textbox)), which range is different from the min and max values of data in the map file (read by python mrcfile). The chimera's range is narrower. - why is that? - I can imagine that chimera apply some cutoff; if this is the case, how can I display the full range of the .map file? Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

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Fitting structures in biological assembly surfaces
by Ahmad Abdelzaher 22 May '18

22 May '18

Hello, I have a structure that generates a surface of the biological assembly. How can I fit this surface with my structures? Regards.

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Re: [Chimera-users] [chimera-dev] Visualize 3D structure of Peptide
by Elaine Meng 22 May '18

22 May '18

Dear Reza, This is not really a Chimera question. You would need to go to the Protein DataBank website and search there. Their searching is powerful and has many options, which you can explore: <https://www.rcsb.org/#Category-search> Another way is to search for your protein of interest at UniProt, then see if there are PDB IDs given in the structures section for that protein. UniProt: <http://www.uniprot.org/> If there isn’t a known structure in the Protein DataBank, other possibilities are to: (A) look in databases of comparative models, e.g. ModBase, from which you can download a PDB file to open in Chimera <https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi> (B) build comparative model yourself if the structure of a similar protein/peptide is known <https://en.wikipedia.org/wiki/Homology_modeling> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> (C) if it’s a pretty small peptide, build from scratch, but still difficult to know if the conformation is realistic without more work (dynamics etc.). For example, Chimera allows you to build peptides (Tools… Structure Editing,... Build Structure; the Start Structure section includes a “peptide” option). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Finally, the chimera-dev e-mail address is for programming questions. If you have user questions, for future reference the better address is chimera-users(a)cgl.ucsf.edu (CC’d on this message). Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 21, 2018, at 10:25 PM, Mohammadreza Behi <m.behi(a)sydney.edu.au> wrote: > > Dear Sir/Madam, > I am trying to visualize a peptide and a protein using Chimera, yet I am not sure if the peptides may have an ID to fetch the structure by ID. > Even I could not find the ID for my protein. > Can you please let me know how I may find the ID for these items? Or if there is not any ID how to visualize them for further studies? > Kind regards, > Reza\

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Hidden capability to compute all bonds on a per-frame basis
by benjamin.horsman＠alumni.ubc.ca 20 May '18

20 May '18

Hello, A 2014 message to chimera-users mentioned that "There is also a hidden capability in Chimera to compute all bonds on a per-frame basis." (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-April/009759.html) Could someone please elaborate on this? Does this functionality still exist is recent versions of Chimera, and has it been documented anywhere? My requirements are just that - to catalogue all (hydrogen) bonds over every frame in a trajectory. Thank you, BGSH

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chimera options opening in tabs and not windows
by Pranav Shah 17 May '18

17 May '18

Dear Developers, I have somewhat of a strange problem with chimera where, different options of the program open into tabs in the same window as opposed to having their own windows. While this is mildly irritating especially when I am using the volume viewer to change the contour level of the map and not being able to visualise the changes in the map as they appear, what gets my goat is that the options/prgorams become unavailable to access when i pull the tab out into its own window. I know this isnt a chimera problem as i have the same issue with other python based programs such as imod and eman. Would you know where i can tweak the preferences so that the programs do not open in tabs but their own independent windows? I appreciate your assistance. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Harvard Medical School 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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Calculating screw transformation between two protein subunits
by Nikita Chopra 17 May '18

17 May '18

Hi I have two protein subunits, which I have aligned along the z-axis. I am considering both the subunits as rigid bodies. Is there a way I could find the screw transformation (rotation along z-axis and displacement along xy plane) between them in chimera ? Thank you for your help.

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Volume viewer levels question
by Markus Heller 15 May '18

15 May '18

Hi all, I have an issue displaying a map file that I opened using the insightgrid.py script. When displaying the grid at the highest level I can get, the levels are still too low, but when I set the levels higher by typing something into the level field (e.g. 1.2e+03 instead of the 1e+03), the levels disappear altogether as shown in the second screenshot. As soon as I adjust the slider, the levels reset to 1e+03. What am I doing wrong? Thanks Markus [cid:image001.png@01D3EC35.74E6A210] [cid:image004.png@01D3EC35.9B86A230]

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