- Chimera-dev - RBVI Mailing Lists

Help with chimera extension for 3D printing
by Stephen Norris 20 Jul '16

20 Jul '16

Hello Chimera developers! I'm a recent graduate of URI where I worked as part of a 3D printing group working on molecular visualization. You can see some examples of our work at http://web.uri.edu/pharmacy/3d/3d-gallery/ . When we started the program we used both Jmol and Chimera on individual models but ever since Tom added the struts commands we've been 100% using Chimera and loving it! However as I'm ending my personal involvement in projects there, I still want to do one last thing which is to solve a major headache for the 3D printing process. When developing model in Chimera we cannot really determine what scale the model and it's components like strut diameter will be when printing. These scales can only really be determined once we import the model into the 3D printing software and set an overall scaling for the model. This is a problem as we can easily make a model which looks nice but when we determine the overall scale the struts may turn out to be too thin, and then we have to go back and re-export the model until we get them acceptable. In addition is no way to relate the scale of a model shown in the viewing window to an actual scale we could input to the computer software. The solution would be to have functionality in Chimera to work with the model and scale things in terms of real-life units. A program like solidworks would easily let one do this but for Chimera units are somewhat arbitrary. One trick with the 3D printing software is that the print bed is shown with a grid of units so we can expand the ortho view until the screen is showing the objects to be printed at their actual real life sizes. I've already developed an extension to do this in Chimera and a side effect is that the scale to input to the printer to get a model at the scale displayed on the screen is easily obtained. I've made a github repo for the extension at https://github.com/gerbi7/UCSF-Chimera-RealScale-Extension . So now I'm running into two problems which could use some expert advice or ideas: 1. It would be good to be able to export models with the scaling pre-applied so that one just has to select the correct unit when importing to the 3D printing software. As far as I can tell most of the export functionality is in C++ and doesn't include support for applying a global scale to an export. Since it's in C++ I don't know if this would be viable as an extension to modify it. So far my idea would be to modify the outputted file? 2. It would be incredibly useful if one could set style parameters such as ribbon width, strut widths, etc in terms of real-life units, and have them stay constant while the user can modify the overall scale of the model by zooming in and out. It would be good if there was some elegant way of doing this instead of brute-force setting every parameter whenever the zoom changes. As a side note if it was possible to just insert a scaling factor whenever an atom coordinate is needed for graphics purposes that would probably work to solve both problems but I doubt that exists currently. I look forward to hearing back from you. Stephen Norris

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Chimera's Amber tools compile on windows
by Abhilash J 23 Jun '16

23 Jun '16

Dear all! I am interested in compiling Amber tools for windows. I tried compiling it from the source code from AMBER website. I was successful for linux and cygwin, But i could not get it to work for windows environment. Few days back i came across chimera. You were able to compile and run the Amber tools code on windows environment. I downloaded and compiled the Amber tools part from the foreign section of the source code. I was unable to get it running on my machine. Also the version was old. In fact i looked at chimera 1.9, it is currently using amber tools 12. I believe the compile might have to do something with cygwin environment and mingw cross platform build. I think there should be patches which help in this build. I am unaware of them. I might be wrong too. All my efforts till now have not yielded a working code on windows.Please let me know what all will be required to compile amber tools on windows, and how i can compile it. I will be grateful if you could help me or point me to the right direction. Thanking you. Regards Abhilash Jayaraj Research Scholar SCFBio Dept. of Chemistry IIT Delhi New Delhi

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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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event loop
by Dougherty, Matthew T 05 Feb '16

05 Feb '16

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 ================================================= =================================================

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Volume Eraser: Recentering the eraser
by Mohan Sudabattula 07 Jan '16

07 Jan '16

Hello, My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? Thank you! Mohan Sudabattula confirm e2a44c6a1c2aa9063cccd37bee44a9add15bde48

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Could I ask some questions about Chimera?
by Archeries 05 Jan '16

05 Jan '16

Hi developers of Chimera, My name is Archeries Ye. I'm a undergraduate from Zhejiang University. These days I have been learning Protein Structure Prediction, and according to my advisor's suggestion, I'm going to study the protein structure prediction function of Chimera. I searched information of Chimera, but unfortunately have not got enough. I wonder if you could spare some time for my questions? 1. Which prediction algorithm does Chimera adapt? Is it independent from protein structure databases? And is it feasible to change the conformation by changing the electric charge of atoms? 2. Could the source code of Chimera be shared for uncommercial use? Thank you for spending your valuable time reading my letter. I will really appreciate for any reply from you. Archeries

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match API change
by Eric Pettersen 21 Dec '15

21 Dec '15

Just a heads up that as a side effect of now reporting both the full and pruned RMSD of an iterated match, the number of return values from Midas.match(), Midas.matchXform(), and MatchMaker.match() changed. The first two added the full RMSD just after the pruned RMSD in their tuple of return values, and the latter did a similar thing, though it returns a list of such (now larger) tuples. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimera-dev] Save the map after hide dust
by Tom Goddard 08 Dec '15

08 Dec '15

Hi Gary, I made it a bit easier to invert the shown portion of the map surface by adding an "sop invertShown" command. It will be in tonight's daily build. So to mask the dust on map #0 you could use sop hideDust #0 size 25 sop invertShown #0 mask #0 #0 invert true Would be nice to make this easier -- maybe in our next generation Chimera. Tom > On Dec 8, 2015, at 6:35 PM, Tom Goddard wrote: > > Hi Gary, > > Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command > > mask #0 sel invert true > > to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. > > Tom > > <surfinvert.py> > > The surfinvert.py script is also on the Chimera Python scripts page > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > > >> On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: >> >> Hi Tom, >> >> 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 a lot >> Gary >> >> >> >> >

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Chimera 2 input devices
by Dougherty, Matthew T 30 Oct '15

30 Oct '15

Under C1 accelerators and some other USB HID activity require the cursor to be on a graphics window. An exception would be the mouse or keyboard interacting with other gui windows such as button pushes or entering file names. For C2 it would be good to have a dedicated input channel independent of the cursor position like the 3dconnexion. The general trend I see with researchers is dual display. One handles graphics and the other gui controls. This gets tricky when s3d is used and the cursor. Is not exactly what. you think (2 visible cursors one active the other inactive) I manage this now with a dedicated chimera extension user gui buttons that rearrange the screens; and with controller mate I can have preconfigured-window-gui-location accelerator commands sent to activate the buttons, at the same time controller mate can set cursor positions and do button pushes. Works for Mac, not an option for PC or Linux. I guess I could set a frame trigger and check a dedicated tcp port, but I am hesitant creating a kludge, because of the underlying strategic design issue and messing with the event loop. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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chimera2 S3D terminology
by Dougherty, Matthew T 29 Oct '15

29 Oct '15

recommend the follow changes to follow HDMI & S3D industry terminology wall-eye stereo ---> SBS-full DTI side by side stereo ---> SBS-half eye separation ---> interaxial distance Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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chimera2 s3d
by Dougherty, Matthew T 27 Oct '15

27 Oct '15

can't remember I mentioned this. on the savepos, it would be good to save the s3d parameters, particularly the interaxial distance. been doing animations where the IA needs to change in order to optimize the S3D effect. sometimes I use unusual values for the parameters. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Linking Chimera with our molecular simulation tool-kit
by Lianheng Tong 22 Oct '15

22 Oct '15

Dear Chimera developers, I am a postdoc research associate working with Prof. Lev Kantorovich of King’s College London. I am currently a full time developer for the ab initio atomic simulation code CP2K, and as a part of our project funding, we are looking to develop a tool kit that would improve user friendliness that would allow the users to construct various bulk or molecular structures in an intuitive and graphically way. We currently have a quite extensive tool-kit (tetr) developed by Prof. Kantorovich for generating, modifying structures—especially tailored for periodic systems, as well as post processing utilities on volume data (such as generating STM images etc). It is written in FORTRAN, and currently is command based only, with the user input being either interactive or by a batch file. The goal, is to be able to link to a visualisation package like Chimera, so that: a) one is able to automatically update the visualisation when the user uses the tool interactively b) allow the user to select atoms and fragments and use these selections as an input to the tool-kit. Ideally, the took-kit can run as an independent code, with the extension providing an interface between Chimera and the tool-kit. The user would then control the tool-kit from within the Chimera command interface. I have used Chimera a lot during my PhD, however, I have not yet written any extension for it. I do, however, have quite a number of years experiences with code development, especially in Fortran and in Python. I am wondering: 1) If you would mind if we develop an extension to link our took-kit with Chimera 2) If the functionalities I mentioned above would be possible to achieve Any suggestions from you would be great. Thank you very much for your time, and I look forward to hearing from you soon. Best regards, Lianheng ==================================== Lianheng Tong Room S4.02, Strand Building Department of Physics Kings College London Strand, London WC2R 2LS, U.K. Tel: +44 20 7848 2064 Fax: +44 20 7848 2420 lianheng.tong(a)kcl.ac.uk ====================================

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binding handlers to SortableTable checkboxes
by Jan Kosinski 17 Oct '15

17 Oct '15

Hi again, How to attach handlers to checkboxes in the CGLtk SortableTable so the handler is invoked automatically when the checkbox is (un)checked? I get it working by subclassing and overriding _widgetCB as below but maybe you have sth more convenient? class ComponentSortableTable(SortableTable): def __init__(self,parent,*args,**kwargs): SortableTable.__init__(self,parent,*args,**kwargs) def _widgetCB(self, datum, column, newVal=None): SortableTable._widgetCB(self, datum, column, newVal=newVal) <my code if column.title == ‘show’: … > Thanks, Jan

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Model panel rename
by Dougherty, Matthew T 15 Oct '15

15 Oct '15

I would like to tie a USB foot pedal to the model panel rename button. I can get the foot pedal signal into my chimera extension. From an extension, what would be the easiest way to Python code the activation of the model panel button? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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adding an exporter
by Dougherty, Matthew T 25 Sep '15

25 Sep '15

I have modified the collada exporter to work with blender to the point I need to fork it off. I want to call it Blender, as opposed to the existing Collada exporter and overwrite that code. It is mostly the collada chimera exporter, but has additional UI inputs to make it better integrate with blender. How do I register it so it lists like the other scene exporters? Is it entirely within the existing collada code extension, or is there another call or init that needs to be made outside the collada extension directory? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Re: [chimera-dev] [Chimera-users] Query related to chimera
by Elaine Meng 31 Aug '15

31 Aug '15

Dear Akalesh Kumar Verma, Sorry no, Chimera does not do protein-protein docking calculations. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 30, 2015, at 3:02 PM, Akhilesh Verma <akhileshverma07(a)gmail.com> wrote: > > Dear Manager, > Is it possible to do Protein protein docking using chimera program? > Your response will be highly appreciated. > Thanking you. > -- > Sincerely yours, > Akalesh Kumar Verma

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