- Chimera-dev - RBVI Mailing Lists

Asking about installation
by Utid Suriya 04 Sep '18

04 Sep '18

Dear, Chimera developer First of all, I would like to introduce myself; I am a graduate student in Thailand and my work is focusing on Drug Discovery. I am interested in using Chimera in visualization so, I downloaded and already installed it by accepting license and condition. However, I cannot open the Chimera program at all. I am not sure what are the related possible problems. One possibility is that I use Window 8. But I am not sure whether it is a bottleneck problem. Thank you very much Utid Suriya Department of chemistry, faculty of science, Chiang Mai university, Thailand 50200

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Re: [chimera-dev] [Chimera-users] Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Thank you very much, Eric. Unhappily I am not familiar with Python scripting, so I will have to wait that someone with that skill adds this useful tool into Chimera code! But for now I will take Elaine's hints! Thank you again Sergio On Tue, Jul 31, 2018 at 3:38 PM Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Sergio, > If you are comfortable writing Python code, there is a provision for > adding custom header types to Multalign Viewer. Look at the MAVHeader > module in your Chimera distribution (<your Chimera>/share/MAVHeader), > particularly the file ChimeraExtension.py which defines headers for charge > variation and CA/backbone/full RMSDs and registers those headers with > Multalign Viewer. I imagine you will have questions (LOL!) so I have > directed responses to the chimera-dev mailing list, which would seem more > appropriate in this case. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Jul 31, 2018, at 11:22 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Sergio, > Sorry, there isn’t a way to automatically make residue attributes into a > header. We had imagined that people would be calculating properties > outside of Chimera, and then using a script or even manually creating a > file in the header format to load them as a header. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/d… > > > > However, you can change the sequence lettering colors to match the ribbon, > so if you first colored ribbon by some residue attribute (with Render by > Attribute or command “rangecolor”), it could be reflected back into the > sequence window in that way. To do that, use sequence window menu > Preferences… Appearance, and then for residue letter coloring (near the > bottom), choose “coloring scheme: ribbon”. I realize this might not be > optimal if some of the coloring makes the letters hard to read. > > I attached an example image with my protein colored by residue average > bfactor (blue -> red -> yellow) and using “ribbon” coloring of the > associated sequence in the alignment. > > With a header you could only have one value per column, but with ribbon > coloring you could have different values (colors) in the same column if > there are multiple structures associated. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <Screen Shot 2018-07-31 at 11.18.18 AM.png> > > > On Jul 31, 2018, at 6:05 AM, Sergio Garay <sergio.alberto.garay(a)gmail.com> > wrote: > > Hi All! > > I would like to know: > Is there any way or tool to write some calculated attribute into a header > format? > > I want to see the same color values obtained for some a calculated > attribute projected onto a sequence. > > I have read in the chimera list the inverse process: exporting a header > from a sequence window to be read as an attribute. > > Thank you in advance. > > -- > Sergio Garay > Dr. en Ciencias Biológicas > Facultad de Bioquimica y Cs. Biológicas > Universidad Nacional del Litoral > Santa Fe - Argentina > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA > Argentina > Ph. +54 (342) 4575-213 > Fax. +54 (342) 4575-221 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Save density map as a mesh
by עמיחי הולצר 30 Jul '18

30 Jul '18

Hi Chimera support, I have 2 questions: 1. How does Chimera calculate the mesh from the density map? 2. How can I save the mesh as a file? Thanks a lot, Amichai Holzer Huji

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Re: [chimera-dev] Dust Clean in cryo-EM maps
by עמיחי הולצר 16 Jul '18

16 Jul '18

Hi, I like the density map after hide density map, is there any way to save the density map after dust hide? Every time I save the density map, it saved the original map instead of density map after hidden dust. Thanks, Amichai 2018-07-13 17:16 GMT+03:00 עמיחי הולצר <amiholz(a)gmail.com>: > Chimera System Hi, > > I am a student in computational structural biology lab in the Hebrew > University of Jerusalem. We are developing software for modelling with electron > microscopy density maps. > > I'm using chimera to display the density maps, and the specific using thr > feature in chimera called clean dust, which shows the map seamlessly. > My question is whether there is a possibility to save the map without the > "dust"? > Because now there is only an option to eliminate dust, but not to save the > clean map. > > Thank in advance, > Amichai Hozler > Hebrew University >

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Visualize 3D structure of Peptide
by Mohammadreza Behi 22 May '18

22 May '18

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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Pointer to model when opened
by Pablo Solar Rodríguez 24 Apr '18

24 Apr '18

Hello Eric and the rest of mates! I would like to know if when you open a PDB through Midas 'open' method, the opened model is returned. I need to have access to that specific model all the time, even when IDs in the Model Panel are changed due to some other models are closed or opened. The idea is something like: if os.path.exists(model_path): from Midas import open self.model_path_pointer = open(model_path, filetype="pdb") And whenever I need, make: self.model_path_pointer.name self.model_path_pointer.id .... *Thank you in advance and kind regards!*

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Renaming a PDB loaded the Model Panel
by Pablo Solar Rodríguez 12 Apr '18

12 Apr '18

Hello all! I am introducing some features in my plugin and I would like to know if there is any smart of way to rename a PDB that is loaded in the Model Panel. I've seen the renameDialog.py module in ModelPanel package but didn't see any way to call it from my plugin. Thank you in advance and kind regards!

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Write-Open
by Pablo Solar Rodríguez 12 Mar '18

12 Mar '18

Hello all! I'm looking to the scripts ( http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/) and can not see a simple example of how to open a PDB. What I need to my extension is to save a PDB relative to a map and then open it to the model panel. Copying it to the model panel does not make sense to me because I need to fix the positions of the moved PDB relative to the map. Could it be something like this? * # Get opened molecule (the one selected in the menu)* * m = self.object_menu.getvalue()* * # Make copy using the copy_molecule native functionality from Chimera* * from Molecule import copy_molecule* * mc = copy_molecule(m)* * # Set copy name* * mc.name <http://mc.name> = m.name.split('.')[0] + '_' + self.chosen_solution + '.pdb'* * copy_path = self.cwd + mc.name <http://mc.name>* * from Midas import open, write* * write(mc, self.map_menu.volume(), self.cwd)* * open(self.cwd)* Thank you in advance!

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cdf output
by White, Tommi A. 05 Feb '18

05 Feb '18

Hello. We are intrigued by a new document format called "CDF". https://www.wolfram.com/cdf/ Are the developers of Chimera... 1) Aware this format exists? 2) Actively seeking ways to output cdf formatted renderings? From a structural biology community standpoint, the ability to break free of the traditional static image figure and have the ability to render in 3D for a more interactive way would be AMAZING for the structural biology community Just wanted to give you a heads up that this exists. If we could output our "images" into cdf files, and further rendered in a document...:) Tommi A. White, Ph.D. Assistant Professor of Biochemistry Director, Electron Microscopy Core Facility University of Missouri W117 Veterinary Medicine Building 1600 East Rollins Street Columbia, MO 65211 573-882-8304 WhiteTo(a)missouri.edu<mailto:WhiteTo@missouri.edu> http://emc.missouri.edu<http://emc.missouri.edu/>

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Running Chimera through Python script
by Evan Seitz 29 Jan '18

29 Jan '18

Hi - I’m trying to follow Example 1 on http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>, but after entering the code precisely as it is written, am getting back the ModuleNotFoundError: No module named ‘chimera’. I’ve tried running the script using both Python2.7 and Python3, and both have resulted in the same error. As a sub-question, is Chimera supported in Python3, or is it best practice to still use Python2? Thank you, Evan Seitz Chimera version: 1.12.0 OS: macOS High Sierra 10.13.2

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