January 2020 - Chimera-dev - RBVI Mailing Lists

Coloring chains from Python
by Jan Kosinski 03 Feb '20

03 Feb '20

Hi, In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures. Best, Jan

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Re: [chimera-dev] monitor suitable for stereo visualization in Chimera
by Tom Goddard 30 Jan '20

30 Jan '20

Hi Wei, The computers can run different operating systems. But almost all VR is done on Windows 10. It can be made to work on Linux and Mac but there are many problems using VR on those operating systems. Tom > On Jan 30, 2020, at 7:35 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > > Tom, > > This is terrific and so exciting! > The movie you attached in the previous email must be what the second person see during a "meeting" session. > About the meeting to sync the to sessions. All the computers have to run on the same type of operating system, ie. > not mixed with PC-Mac-Linux, right? > > I am happy I reached out to the Chimera group about stereo display and now see this new opportunity. > > Thanks! > > Wei > > > > > > > >> On Thu, Jan 30, 2020 at 8:34 PM Tom Goddard <goddard(a)sonic.net> wrote: >> Hi Wei, >> >> We do routinely do 2 person VR sessions, and have sometimes done 3 or 4. Each VR headset has to be connected to a separate computer. This is a limitation of the current VR driver technology where it only allows communicating with one attached headset. So for two or more people, each start ChimeraX and VR on separate computers and use a command "meeting" to sync the to sessions. Each person sees the other persons VR hand controller cones and an image of the other person's face and these track the person's movement so it is easy to point to parts of the structures, and each person can move the models and change them. I should make a video showing multiperson VR like that opioids video. Here is another VR video that shows some 2 person VR >> >> https://www.youtube.com/watch?v=S4lDzUEUFL0&feature=youtu.be >> >> More about VR for molecules and cells is at the UCSF VR web site >> >> https://vr.ucsf.edu >> >> I develop the ChimeraX VR capabilities and they have a long ways to go, but also a lot of potential. The RTX 2080 Ti is the best graphics you can get for VR. >> >> Tom >> >> >>> On Jan 30, 2020, at 6:14 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >>> >>> Tom, >>> >>> This movie itself is magic! You can merge the operator with the molecule in the movie ---- VR world and the real world are merged together, that is amazing! >>> >>> It is so delightful to see this movie, making me want to go away from the old system right now and embrace the new one. >>> >>> With the VR system, is it possible to have two people see the same view of the object as we did with the old system? I guess it takes two sets of VR system, but without a mouse cursor, how can we see the same view and points to the same place? >>> >>> Thanks so much for the detailed and professional description about old and new stereo systems. I guess when the old technology is dying out, we have no choice but to keep up with the trend. I have to read and learn more in order to make a wise decision. Your email is a good start. >>> >>> Thank you, >>> >>> Wei >>> >>> >>>> On Thu, Jan 30, 2020 at 6:49 PM Tom Goddard <goddard(a)sonic.net> wrote: >>>> Hi Wei, >>>> >>>> Unfortunately stereoscopic visualization is dying out, hardware vendors are not supporting it. Nvidia 3D Vision which was LCD shutter glasses that worked with many gaming displays (fast refresh displays, e.g. 120 Hz or 144 Hz) was dropped by Nvidia last April, they removed support for it from their graphics drivers. The Zalman row interleaved displays were discontinued long ago. Here is old info about Nvidia 3D for Chimera, and also old information about PyMol stereo display >>>> >>>> https://www.rbvi.ucsf.edu/Outreach/technotes/3dvision.html >>>> >>>> https://pymolwiki.org/index.php/Stereo_3D_Display_Options >>>> >>>> We still have a stereo projector system working with Chimera and ChimeraX that uses RealD CE4S LCD shutter glasses (http://www.colorlinkjapan.com/brand/product/ce4s.html) and an old StereoGraphics EXXR IR emitter (http://www.ultimate3dheaven.com/crst.html). The emitter connects to a 3-pin DIN connector available on some old Nvidia Quadro graphics cards. We use a P6000 which has a daughter board to provide the 3-pin DIN signal that syncs the glasses with the left and right eye displayed images. I'm not sure any of this is sold anymore, but maybe you could get it and maybe it would work, but not with 2080Ti graphics. >>>> >>>> We use virtual reality for stereoscopic display in ChimeraX (https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html). Here's a YouTube video showing it being used (https://www.youtube.com/watch?v=FCotNi6213w). This isn't very similar to the older stereo systems because it blocks your view of everything and requires all new user interface since you can't use the mouse and keyboard easily with VR. But it does provide even better stereoscopic depth perception than the old systems. >>>> >>>> In short, you can probably do old stereo with lcd or polarized glasses if you are going to go to a great deal of trouble working with unsupported hardware. Since no one uses this stuff, the graphics drivers also have lots of trouble delivering the images -- we have problems every year keeping our stereo projection system working in the face of updated graphics drivers that no longer work with stereo and 2 displays. >>>> >>>> If you still want to pursue the old stereo, Ken Satuyshur at University of Wisconsin has a few systems working and you could ask him for more info. >>>> >>>> Tom >>>> >>>> >>>>> On Jan 29, 2020, at 7:57 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >>>>> >>>>> Hi Elaine and Tom, >>>>> >>>>> I am trying to build a GPU workstation that mostly focuses on computation, ie. I want to have 4 2080Ti GPU cards. But I think these GPU cards do not support 3D visualization. One colleague of mine has such a workstation and he uses Zaleman monitor and can display the stereo map using Chimera. Zakeman monitor is out of market for a number of years, I am wondering if you are aware of any other type monitor that can be used for this purpose. >>>>> >>>>> Thank you, >>>>> >>>>> Wei >>>>> _______________________________________________ >>>>> Chimera-dev mailing list >>>>> Chimera-dev(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >>>> >>

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Re: [chimera-dev] monitor suitable for stereo visualization in Chimera
by Tom Goddard 30 Jan '20

30 Jan '20

Hi Wei, We do routinely do 2 person VR sessions, and have sometimes done 3 or 4. Each VR headset has to be connected to a separate computer. This is a limitation of the current VR driver technology where it only allows communicating with one attached headset. So for two or more people, each start ChimeraX and VR on separate computers and use a command "meeting" to sync the to sessions. Each person sees the other persons VR hand controller cones and an image of the other person's face and these track the person's movement so it is easy to point to parts of the structures, and each person can move the models and change them. I should make a video showing multiperson VR like that opioids video. Here is another VR video that shows some 2 person VR https://www.youtube.com/watch?v=S4lDzUEUFL0&feature=youtu.be <https://www.youtube.com/watch?v=S4lDzUEUFL0&feature=youtu.be> More about VR for molecules and cells is at the UCSF VR web site https://vr.ucsf.edu <https://vr.ucsf.edu/> I develop the ChimeraX VR capabilities and they have a long ways to go, but also a lot of potential. The RTX 2080 Ti is the best graphics you can get for VR. Tom > On Jan 30, 2020, at 6:14 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > Tom, > > This movie itself is magic! You can merge the operator with the molecule in the movie ---- VR world and the real world are merged together, that is amazing! > > It is so delightful to see this movie, making me want to go away from the old system right now and embrace the new one. > > With the VR system, is it possible to have two people see the same view of the object as we did with the old system? I guess it takes two sets of VR system, but without a mouse cursor, how can we see the same view and points to the same place? > > Thanks so much for the detailed and professional description about old and new stereo systems. I guess when the old technology is dying out, we have no choice but to keep up with the trend. I have to read and learn more in order to make a wise decision. Your email is a good start. > > Thank you, > > Wei > > > On Thu, Jan 30, 2020 at 6:49 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Wei, > > Unfortunately stereoscopic visualization is dying out, hardware vendors are not supporting it. Nvidia 3D Vision which was LCD shutter glasses that worked with many gaming displays (fast refresh displays, e.g. 120 Hz or 144 Hz) was dropped by Nvidia last April, they removed support for it from their graphics drivers. The Zalman row interleaved displays were discontinued long ago. Here is old info about Nvidia 3D for Chimera, and also old information about PyMol stereo display > > https://www.rbvi.ucsf.edu/Outreach/technotes/3dvision.html <https://www.rbvi.ucsf.edu/Outreach/technotes/3dvision.html> > > https://pymolwiki.org/index.php/Stereo_3D_Display_Options <https://pymolwiki.org/index.php/Stereo_3D_Display_Options> > > We still have a stereo projector system working with Chimera and ChimeraX that uses RealD CE4S LCD shutter glasses (http://www.colorlinkjapan.com/brand/product/ce4s.html <http://www.colorlinkjapan.com/brand/product/ce4s.html>) and an old StereoGraphics EXXR IR emitter (http://www.ultimate3dheaven.com/crst.html <http://www.ultimate3dheaven.com/crst.html>). The emitter connects to a 3-pin DIN connector available on some old Nvidia Quadro graphics cards. We use a P6000 which has a daughter board to provide the 3-pin DIN signal that syncs the glasses with the left and right eye displayed images. I'm not sure any of this is sold anymore, but maybe you could get it and maybe it would work, but not with 2080Ti graphics. > > We use virtual reality for stereoscopic display in ChimeraX (https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html>). Here's a YouTube video showing it being used (https://www.youtube.com/watch?v=FCotNi6213w <https://www.youtube.com/watch?v=FCotNi6213w>). This isn't very similar to the older stereo systems because it blocks your view of everything and requires all new user interface since you can't use the mouse and keyboard easily with VR. But it does provide even better stereoscopic depth perception than the old systems. > > In short, you can probably do old stereo with lcd or polarized glasses if you are going to go to a great deal of trouble working with unsupported hardware. Since no one uses this stuff, the graphics drivers also have lots of trouble delivering the images -- we have problems every year keeping our stereo projection system working in the face of updated graphics drivers that no longer work with stereo and 2 displays. > > If you still want to pursue the old stereo, Ken Satuyshur at University of Wisconsin has a few systems working and you could ask him for more info. > > Tom > > >> On Jan 29, 2020, at 7:57 PM, Wei Zhang <zhangwei(a)umn.edu <mailto:zhangwei@umn.edu>> wrote: >> >> Hi Elaine and Tom, >> >> I am trying to build a GPU workstation that mostly focuses on computation, ie. I want to have 4 2080Ti GPU cards. But I think these GPU cards do not support 3D visualization. One colleague of mine has such a workstation and he uses Zaleman monitor and can display the stereo map using Chimera. Zakeman monitor is out of market for a number of years, I am wondering if you are aware of any other type monitor that can be used for this purpose. >> >> Thank you, >> >> Wei >> _______________________________________________ >> 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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monitor suitable for stereo visualization in Chimera
by Wei Zhang 30 Jan '20

30 Jan '20

Hi Elaine and Tom, I am trying to build a GPU workstation that mostly focuses on computation, ie. I want to have 4 2080Ti GPU cards. But I think these GPU cards do not support 3D visualization. One colleague of mine has such a workstation and he uses Zaleman monitor and can display the stereo map using Chimera. Zakeman monitor is out of market for a number of years, I am wondering if you are aware of any other type monitor that can be used for this purpose. Thank you, Wei

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Re: [chimera-dev] Update to DelphiViewer Chimera plugin
by Tom Goddard 17 Jan '20

17 Jan '20

Hi Emil, We will update Chimera to use CUBE format with DelPhi before our next release. The link I sent you to the Chimera bug report gives the full DelPhi output and DelPhi version that produced the incorrect file. http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169> I've attached it here as a text file. I asked the user to contact your lab a several days ago but I don't know if they have time. Thanks! Tom > On Jan 8, 2020, at 9:56 AM, Emil Alexov <ealexov(a)g.clemson.edu> wrote: > > Hi Tom, > > Please switch to CUBE format. Regarding the user, who knows how the file was generated. Let them contact us and we will figure out what was wrong. In any case, I agree with you that wrong format file should not be generated. Ask the user to contact us and we will let you know the outcome. > > Emil > > On Wed, Jan 8, 2020 at 12:33 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Emil, > > I agree it is probably a misunderstanding. The CUBE format is fine and I can switch new Chimera versions to use it. The trouble is that a user sent me a *.phi file written by DelPhi 7 that does not follow the format specification for .phi. > > <http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.…>http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.… <http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.…> > > as part of Chimera bug report > > http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169> > > This is a binary file so it is not an ascii CUBE file. Looking at the strings at the beginning of the file it appears to be .phi format without required record lengths. If this change to the DelPhi .phi file output was not intended then either it should be fixed to output a correct .phi format, or DelPhi should be made to not output .phi at all (just give an error that it is no longer supported). As it is now, DelPhi outputs an incorrect file. > > Tom > > >> On Jan 8, 2020, at 3:48 AM, Emil Alexov wrote: >> >> Tom, >> >> This seems to me is misunderstanding. We purposely decided to make the new delphi version to write PHI map file into CUBE format, because this is the format that all existing visualization packages take. This is documented in DelPhi manual and nowadays our users indeed prefer CUBE format versus the old style binary file. >> >> However, if this is too much trouble for Chimera maintenance and development, we will make an effort to include binary option in the new delphi. Let's us know what are your thoughts about this. >> >> Emil Alexov >> >> On Tue, Jan 7, 2020 at 6:38 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Shailesh, >> >> Thanks. I see your changes to the Chimera DelphiViewer plugin make it write out a Gaussian cube file instead instead of a .phi file. While that helps a little it would be much better if new DelPhi wrote out a .phi file following the online documentation for that file format. This should be trivial to do even from C++ (while the original format used Fortran records, they are just a 4 byte count for each record, followed by the binary data). Having DelPhi write out a different incompatible .phi file as it dose not breaks all software that used that format. We can't take the tens of thousands of copies of Chimera out of circulation that read .phi files. Also even with your change to make Chimera run DelPhi outputting a cube file, users will run DelPhi outside of Chimera, then try to open the .phi file and get an error. >> >> If the .phi format is just going to remain broken with new DelPhi versions writing an incompatible format I think we just need to remove it from Chimera and our new program ChimeraX. If your new .phi format is in use by new software and cannot be fixed I'd suggest that you use a different file suffix so software can correctly read the new or old format. >> >> Tom >> >> >>> On Jan 7, 2020, at 10:55 AM, Shailesh Kumar Panday wrote: >>> >>> Hello Chimera Developers, >>> >>> We have made some changes in the DelphiViewer plugin to enable reading and writing Delphi potential in "Gaussian cube grid" format. The older binary "Delphi or GRASP potential" format files are no longer supported in Delphi. Hence plugin was unable to parse the potential file, the attached version fixes this issue. >>> >>> Thank you, >>> >>> Shailesh Kumar Panday >>> Postdoctoral Fellow >>> Computational Biophysics and Bioinformatics Lab >>> Department of Physics and As >>> Clemson University, SC 29634 >>> Lab: http://compbio.clemson.edu <http://compbio.clemson.edu/> >>> <DelphiViewer.tar>_______________________________________________ >>> 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> >> >> >> -- >> Emil Alexov >> Professor, Department of Physics >> Professor, Department of Material Sciences >> Professor, School of Nursing: Healthcare Genetics >> Faculty Scholar at Clemson School of Health Research >> Clemson University >> Lab: http://compbio.clemson.edu <http://compbio.clemson.edu/> > > > -- > Emil Alexov > Professor, Department of Physics > Professor, Department of Material Sciences > Professor, School of Nursing: Healthcare Genetics > Faculty Scholar at Clemson School of Health Research > Clemson University > Lab: http://compbio.clemson.edu <http://compbio.clemson.edu/>

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About debugging in chimera
by 张双博 13 Jan '20

13 Jan '20

Dear Sir/Madam, I am trying to debug one of the existing plugins to help my understanding of how to write my extension. Usually, I would place "import pdb; pdb.set_trace()" in some lines of the program where I am interested and run it. And when the program encounters this line, it will stop, so I can go through line by line to follow the logic of this python program, which is really helpful. However, when I did this to one plugin of chimera, the plugin and chimera seems frozen, I mean, both didn't respond and there is no "(Pdb)" prompt in opening shell as normally did. I tried this in different places in different scripts, none worked. So I would like to ask how to enable this feature in Chimera or are there some other ways for debugging in Chimera? Sincerely, Shuangbo

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Update to DelphiViewer Chimera plugin
by Shailesh Kumar Panday 08 Jan '20

08 Jan '20

Hello Chimera Developers, We have made some changes in the DelphiViewer plugin to enable reading and writing Delphi potential in "Gaussian cube grid" format. The older binary "Delphi or GRASP potential" format files are no longer supported in Delphi. Hence plugin was unable to parse the potential file, the attached version fixes this issue. Thank you, Shailesh Kumar Panday Postdoctoral Fellow Computational Biophysics and Bioinformatics Lab Department of Physics and As Clemson University, SC 29634 Lab: http://compbio.clemson.edu<http://compbio.clemson.edu/>

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using chimera to display tomography map
by Wei Zhang 02 Jan '20

02 Jan '20

Hello, Happy 2020! We are doing tomography reconstruction of retrovirus assemblies. Because the raw tomograms are very noisy, they can not be represented nicely using isosurfaces. I see other researchers in the field presented the tomo map in Chimera by superimposing subtomogram-averaged map onto the original tomogram according to the subunit's locations and relative orientations. The color of the displayed subunits is based on the correlation coefficient between the averaged subunit map and the original density of the tomogram. One example is Fig.1B in this paper: https://advances.sciencemag.org/content/5/11/eaaw3631 We do use the program Dynamo for the subtomogram averaging procedure, so our data format is very similar to what was used in this paper. Is this feature is part of Chimera? Could we obtain the extended software? Or is this customer built and we need to contact the authors of the paper? Or shall we work out this procedure by ourselves with the help of Chimera experts? Thank you, Wei

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Chimera-dev January 2020