- Chimera-dev - RBVI Mailing Lists

icosahedron with a T number
by Wei Zhang 10 Apr '20

10 Apr '20

Hello, I have been playing with the icosahedron utility in Chimera. I really like this feature, especially with the sphere factor. The current routine uses a subdivision factor to represent the number of triangles on an icosahedral surface. However this lattice is not the same as we see in icosahedral viruses, which use a T number to designate symmetry. With a subdivision number, there are always hexamers on any edge of the icosahedron, whereas in the virus structure this is not the case. I am wondering if Chimera has an utility that can use the T number as the basis for building an icosahedron surface. Thank you. Hope everything is going well and stay safe! Wei

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Drawing crystal structures
by Chai, Wern Chern - chawy134 06 Apr '20

06 Apr '20

Hi there, Hope you are well. I'm struggling to draw my protein structure (no known PDB). I've searched online for manuals, guides etc. but can't seem to find any help. It will be much appreciated if you could guide me on how to do this, or point me in the right direction. In the meantime, stay safe! Thank you. Regards, WC Chai @ Brian Chia

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Mac Installation error
by Blend Fathullah 17 Mar '20

17 Mar '20

Hello, I have MacBook Air and tried to install Chimera software, the Mac as show an error and says that it can’t be installed (kindly find attached screenshot). Please can you advise me on how to fix this issue? Kind regards, Blend Fathullah MSc student/ Drug Discovery and Pharmaceutical Science School of Pharmacy University of Nottingham NG7 2RD, United Kingdom This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Get Molecule Index in Model Panel
by Pablo Solar Rodríguez 29 Feb '20

29 Feb '20

Hello all, Optimizing my plugin, I need to hide atoms and show ribbons for some opened Molecules. What I am trying is to loop over opened molecules in the ModelPanel and, If the Molecule matches a specific tag, save its index in a indexes list. Then, hide atoms and show ribbons by makeCommand with the indexes: *def adjust_visualization(self, final_pdbs):* * """ Adjust atoms and ribbons visualization for FitOpt final solutions """ indexes = [] chimera.openModels.add(final_pdbs) molecule_list = om.list(modelTypes=[Molecule])* * for index, molecule in enumerate(molecule_list):* * if self.fitopt_tag in molecule.name <http://molecule.name>: indexes.append('#' + str(index))* * makeCommand(' '.join(['~show', ' '.join(indexes)])) makeCommand(' '.join(['ribbon', ' '.join(indexes)]))* It seems that the index from enumerate is not corresponding to the index in the ModelPanel so how could I get the proper molecule index?? Thank you all in advance! Regards!! *Pablo Solar Rodríguez*

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copy_molecule does not keep representation
by Pablo Solar Rodríguez 28 Feb '20

28 Feb '20

Hello all again!! I am using the copy_molecule from Molecule ( http://www.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/copymol.py) but when I add the new pdb to the ModelPanel it is in atoms view and grey-colored. For example, if I copy 5 pdbs that are in ribbons view, the new 5 pdb copies will be opened in atoms view and all in grey color. Is normal this behaviour when using copy_molecule? Is there a way to fix this? Thank you in advance!

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Unsubscribe from the mailing list
by Daniel Viladrich Herrmannsdoerfer 28 Feb '20

28 Feb '20

Hi, Could you please unsubscribe me from the Chimera mailing list? Thanks, Daniel Viladrich Herrmannsdoerfer

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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 31 Jan '20

31 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 31 Jan '20

31 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 31 Jan '20

31 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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