July 2018 - Chimera-dev - RBVI Mailing Lists

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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