- Chimera-dev - RBVI Mailing Lists

big volume data
by Dougherty, Matthew T 03 Jun '16

03 Jun '16

I have a 80GB tomogram. Is there a way to read it into chimera, such as the chimera map format & chunking, or some multiscale feature? Viewing entire volume at low resolution subsampling as a starting point, then be able to zoom into a ROI for maximum resolution is desired. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Chimera Model Panel Grouping
by Taylor Gerpheide 20 May '16

20 May '16

I'm working on an extension which needs to be able to group certain open models like the model panel does. Is there a way to utilize the group function in the model panel from an extension in python? Thank you, Taylor

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Chimera extension threads
by Tanja Štular 18 May '16

18 May '16

Dear Sir or Madam, I have been developing an extension for UCSF Chimera. I'm wondering if there is any option for background threading for loading object to Chimera view? Our plugin allows loading large molecules to Chimera which sometimes causes freezing of Chimera and plugin for a little time. I know about Subprocess class ( https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_RunSub…) but it doesn't seem to work (same goes for python threading). Thank you in advance. Best regards, Tanja

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Re: [chimera-dev] suggestions for better STL export - remove internal, reduce atom vertices
by Tom Goddard 09 May '16

09 May '16

A number of web sources say the program netfabb can “repair" surface meshes. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008826.html https://thingiverse-production-new.s3.amazonaws.com/assets/35/64/72/a2/77/E… Tom > On May 9, 2016, at 12:32 AM, Jakob Suckale <jakob.suckale(a)uni-tuebingen.de> wrote: > > Dear all, > > A follow up on Tom's suggestion. I have tested MeshLab. It does indeed have functions that can be used to reduce internal surfaces (https://www.youtube.com/watch?v=9EHJQd3SREE <https://www.youtube.com/watch?v=9EHJQd3SREE>) but it's far from a good solution. It is based on assigning a value to vertices based on visibility (Ambient Occlusion) and then removing the ones that have low scores. In a ribbon model, however, it often opens holes for example on the inside of a helix and it leaves many internal structures untouched. > > All the best, > > Jakob > > On 15 April 2016 at 21:29, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Jakob, > > We discussed the excessive STL vertices in atoms and bonds last week and I put a fix into the daily build and release candidate. > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html> > > Apparently you are not using those versions since your images show the high vertex density. I’ve attached an image using the current Chimera release candidate that shows reasonable vertex density. > > Unfortunately eliminating internal structures and stitching together meshes for atoms, bonds and ribbons at the seams is very difficult. Yes $10000 CAD software packages can do it but we don’t have the resources to solve that problem. Since every 3d printer has to deal with this problem I expect the printer software to be able to handle it, but perhaps it is too hard a problem for the 3d printer companies as well. Perhaps there is free software that can eliminate internal structures and stitch mesh intersecting edges together, I have not researched it — I’d start looking at MeshLab. > > Tom > > <stl_mesh.png> >> On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote: >> >> Dear Chimera developers, >> >> Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. >> >> >> 1 - Remove invisible internal and therefore unnecessary structures. >> >> Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). >> <Screen Shot 2016-04-15 at 13.24.44.png> >> as well as copious amounts of invisible internal surfaces for wire and ball and stick models. >> <Screen Shot 2016-04-15 at 13.27.36.png> >> If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. >> >> >> 2 - Reduce the number of vertices for atom models. >> >> Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. >> >> Best regards, >> >> >> Jakob Suckale, PhD >> Lecturer in Biochemistry >> University of Tübingen >> +49-7071-29-73363 <tel:%2B49-7071-29-73363>_______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > >

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Run Delphi Controller with Chimera on Mac
by Mirco Dindo 02 May '16

02 May '16

Dear Chimera dev, just a question to use the delphi controller with Chimera on MAC. I didn't find anything in the forum about it. The problem is: which file needs delphi to start the calculation? I downloaded the package to run Delphi with Chimera on Mac, and after initialization and preparation of different parameters to start the calculation I cannot find the Delphi Executable. Which is the file to connect the Delphi Controller for Mac? Thanks in advance, Best, Mirco

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Labeling and coloring chains
by Deniz Simsek Buck 27 Apr '16

27 Apr '16

Hi, I am very new to Chimera. If you have time, I would really appreciate your answers. I am working with a structure that contains 80 chains. 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. How do I do this? 2. Also, I would like to add labels to the individual chains I choose on the structure. How do I do this? Thank you, Deniz

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suggestions for better STL export - remove internal, reduce atom vertices
by Jakob Suckale 15 Apr '16

15 Apr '16

Dear Chimera developers, Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. 1 - Remove invisible internal and therefore unnecessary structures. Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). [image: Inline images 1] as well as copious amounts of invisible internal surfaces for wire and ball and stick models. [image: Inline images 2] If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. 2 - Reduce the number of vertices for atom models. Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. Best regards, Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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surface calculation failed, mscalc returned code -11
by Sunny Sharma 07 Apr '16

07 Apr '16

Hi, I have been trying to generate a surface model of a relatively larger molecule yet a single chain and have been getting the error (surface calculation failed, mscalc returned code -11). I have tried several options like splitting but have failed to get rid of this error and generate the surface model. Looking forward to your help Best Regards Sunny -- Sunny Sharma, PhD RNA Molecular Biology FRS/F.N.R.S. Université Libre de Bruxelles Rue Profs Jeener & Brachet, 12 B-6041 Gosselies, Belgium. Mobile: +32 484656127

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a more logical command for atom view
by Jakob Suckale 04 Apr '16

04 Apr '16

Dear Chimera dev't team, As a new user to Chimera, I always found the command to show atoms counterintuitive and I would like to suggest to add a synonym that is logically consistent with the other options to show a molecule. How about "atom achain"? If you asked any new user to complete the following series, the answer would not be "display" - surface achain, ribbon achain, ? achain. This is probably not something that veterans of Chimera still notice but it's illogical to new users and could be easily remedied with a synonym in addition to "disp". This wouldn't affect any old users while being consistent and logical. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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Re: [chimera-dev] event loop
by Greg Couch 05 Feb '16

05 Feb '16

For me, the event loop version is conceptually simpler because it is integrated with the mechanism that dispatches mouse events. But that means to you need to understand how to integrate it with the application event loop, where the details vary with which GUI toolkit is used. The ReadStdin version just uses Chimera abstractions, so that is very appealing. Both techniques will work with ChimeraX. -- Greg On 2/5/2016 11:31 AM, Dougherty, Matthew T wrote: > > I am leaning toward this > > An alternative would be to use threads where the queue is checked > every frame. See ReadStdin/__init__.py for details there. > > > any advantage of one over the other? > > will this work for chimera2? > > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > > > ------------------------------------------------------------------------ > *From:* Greg Couch <gregc(a)cgl.ucsf.edu> > *Sent:* Friday, February 5, 2016 1:05 PM > *To:* Dougherty, Matthew T; chimera-dev(a)cgl.ucsf.edu > *Subject:* Re: [chimera-dev] event loop > Use the (Tcl) event loop. If you run the interface in a separate > process, then you have chimera's event loop invoke a callback when > there is data to be read on the socket connecting the two processes. > That is what's done to implement the --send command line option. See > DBPuppet/tcl_sockets.py for details. > > An alternative would be to use threads where the queue is checked > every frame. See ReadStdin/__init__.py for details there. > > HTH, > > Greg > > On 2/4/2016 2:37 PM, Dougherty, Matthew T wrote: >> >> I am working on a human interface for volume rendering. >> >> >> The livid ds1 mixer uses midi through USB. >> >> http://lividinstruments.com/products/ds1/ >> >> >> I should be able to use python midi libraries for access. >> >> >> This leads to the problem of the midi implementation, and a question >> as to a similar implementation for chimera2. >> >> >> One implementation would insert into the event loop, another approach >> could be tied to a frame/trigger callback. >> >> >> Any suggestions? >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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