- Chimera-dev - RBVI Mailing Lists

Get Molecule Index in Model Panel
by Pablo Solar Rodríguez 28 Feb '20

28 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 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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Broken Python Resource?
by Kevin Manning 18 Nov '19

18 Nov '19

Hi, Kevin here from Comparitech. Just wanted to let you know about a broken link I found here - http://preview.cgl.ucsf.edu/chimera/data/downloads/1.1700/docs/ProgrammersG… The Python tutorial link (http://www.python.org/doc/current/tut/tut.html) isn’t working, if you are still updating your page, the new tutorial link is here https://docs.python.org/3/tutorial/ Perhaps you’d also consider adding a link to the Python cheat sheet my colleague Tim just finished - https://comparite.ch/python-cs Hope this helps. Thanks! Kevin PS. If you’re not interested just let me know and you won’t hear from me again. Kevin Manning Comparitech - tech compared and reviewed Comparitech is owned and operated by Comparitech Limited, company no. 09962280, Kings Lodge, London Road, West Kingsdown, Sevenoaks, Kent, TN15 6AR United Kingdom. Telephone +44(0)333 577 0163

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An online extension download instruction
by Deng Chengtian 18 Oct '19

18 Oct '19

Hi, I am trying to run an existing extension but it generate an error [error2] such that the file”<chimera directory>\share\chimeraInit.py,” line 259, in create process. Could you let me know what is potentially happening? The extension I dowloaded were created according to the instruction, but I don’t know if it is because a version conflict or maybe it s because it wasn’t dowloaded into a correct location? The plug-in seems successfully loaded into chimera and have its own window under tools/utilities. Best regard, Jeremy Deng

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Divided the Volume Data into two parts
by Huiya Zhou 23 Aug '19

23 Aug '19

Hello, I would like to divided a density map (volume data) into two parts. For example, the size of the whole density map is 320*320*320. I want to get one part which covers the region from (i,j,k) to (x,y,z), e.g. from (0,0,0) to (100,100,100). The rest is the other part. The transparency for the first part is 0 and for the second part is 0.5. And I still want to get the histogram of the first part. How could I achieve this in a python script? Actually, I want to get the histogram of different regions. I plan to run a loop for different regions (Change the (i,i,k) and (x,y,z) for the first part). Could I save all of the histograms in one file which is not a window of the Chimera but a picture. Best, Huiya

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New Chimera extension
by mohmed badr 19 Aug '19

19 Aug '19

Greeting I want to create new chimera extension, that ease the user interaction with chimera, thus I will need to send the extension to many tester and get their feedback. If I understand the license agreement correctly, it stated that I can not distribute any edited version of chimera without your permission, does this include chimera extension too, and if it does please direct me to the person who can give me permission (if it's not you), please note this is my first time to develop chimera extension, if there is any other legal matter I should be aware of please stated as well. Regards Mohamed Badr

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volume.py -> xyz_bounds
by Ryan Harlich 23 Jul '19

23 Jul '19

Hi Dev Team, I had a question about how to use the method xyz_bounds in volume.py. I want make an pdb structure with 3 atoms that makes the same bounding box as a surface. So given a surface I want to use xyz_bounds to the it’s max x,y,z. Which I believe would be xyz_max – xyz_min. Still I do not know how to use xyz_bounds. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Multiple copies using Unit Cell function
by Sunandan Mukherjee 09 Jul '19

09 Jul '19

Dear Chimera developers, I want to generate crystallographic unit cells using information in PDB files with help of Unit Cell function from a script (executed with /chimera --nogui/) with the following options: Cell origin 0 0 0; Number of cells 2 2 2 and offset 0 0 0. Basically, I need to generate a block consists of multiple unit cells from a script. Please help me. Thanks in advance! With regards, Sunandan

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Loop refinement in chain A and Chain B
by Aashish Bhatt 06 May '19

06 May '19

Dear Sir/ Ma'am I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. Can you please give me an idea of how to build the complete structure? Best regards Aashish INST-Mohali India

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About Chimera Extension Permission
by Yuhong Zha 25 Mar '19

25 Mar '19

Dear Sir or Madam, This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are currently developing a Chimera extension to implement our MAINMAST algorithm. However, when I update my Chimera to the newest version, I started to get permission errors. I'm using a Mac. In our extension, we have some code involving editing files like "os.remove(filename)". However, after the update, the extension receives error "Operation not permitted" when executing those lines. I think one possible reason might be improper updating steps. After the update, I started Chimera directly from installer instead of drag the icon to my folder. Then this error occurs. Later, even when I deleted the Chimera by dragging it to trash and deleting trash, and then re-download and install Chimera, the error still occurs. We have 2 Mac made the update but only one of them has this error. Do you have any clue why this happens? Thank you in advance for your help and looking forward to your reply! If there is any question regarding our extension, please let me know! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Re: [chimera-dev] Retrieving model_id / model_name via API
by Tom Goddard 07 Mar '19

07 Mar '19

Oops. Should be v.new_region(ijk_step = (1,1,1), adjust_step = False) Chimera automatically adjust the step size to stay within a maximum total number of voxels. The adjust_step = False means not to do that automatic changing of the specified step. Tom > On Mar 7, 2019, at 2:57 PM, Lars Hangartner <lhangart(a)scripps.edu> wrote: > > Hi Tom. > > Thanks for the reply. Unfortunately, this did not work. My implementation was as follows and did not change anything. > Best, > Lars > > for vol in openModels.list(modelTypes=[Volume]): > vol.new_region(ijk_step = (1,1,1)) > > > >> On Mar 7, 2019, at 1:07 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> To set the step of a Volume model v in Chimera in Python code >> >> v.new_region(ijk_step = (1,1,1)) >> >> Tom >> >> >>> On Mar 6, 2019, at 8:42 PM, Lars Hangartner <lhangart(a)scripps.edu <mailto:lhangart@scripps.edu>> wrote: >>> >>> Hi Eric, >>> >>> Thanks for the swift response, worked like a charm. May I also ask how to set the ’step’ property value from the volume viewer GUI pop-up from a script? >>> >>> Thanks, >>> >>> Lars >>> >>>> On Mar 6, 2019, at 3:40 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Lars, >>>> The model attributes for the ID are ‘id’/‘subid’ for the parts before and after any ‘.’ respectively, and the ‘name’ attribute has the model name. You would loop through all volume models with something like: >>>> >>>> from chimera import openModels >>>> from VolumeViewer import Volume >>>> for vol in openModels.list(modelTypes=[Volume]): >>>> print “%d.%d %s” % (vol.id <http://vol.id/>, vol.subid, vol.name) >>>> >>>> We realize the programmer documentation isn’t great. What little we have you can find here: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> . One of our objectives for ChimeraX is much better programmer documentation. >>>> >>>> —Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> >>>> >>>>> On Mar 6, 2019, at 10:40 AM, Lars Hangartner <lhangart(a)scripps.edu <mailto:lhangart@scripps.edu>> wrote: >>>>> >>>>> Hi guys, >>>>> >>>>> I am desperately looking to get the model_id / model name from all open volume objects. I have tried openModel.list()[0].model_id in many iterations but no success… I would like to iterate through models and identify the resampled ones. >>>>> >>>>> Can anybody help? >>>>> >>>>> Thanks, >>>>> >>>>> Lars >>>>> >>>>> >>>>> P.S: API documentation would really be helpful. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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> >>>>> >>>> >>> >>> _______________________________________________ >>> 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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Retrieving model_id / model_name via API
by Lars Hangartner 07 Mar '19

07 Mar '19

Hi guys, I am desperately looking to get the model_id / model name from all open volume objects. I have tried openModel.list()[0].model_id in many iterations but no success… I would like to iterate through models and identify the resampled ones. Can anybody help? Thanks, Lars P.S: API documentation would really be helpful.

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rc(command): save session command problem
by Yuhong Zha 28 Feb '19

28 Feb '19

Dear Sir or Madam, This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are currently developing a Chimera extension to implement our MAINMAST algorithm. However, we encountered a problem of using Chimera's command line "rc("save current_session.py")" to save current session. This problem only happens in some Mac system. In our extension, we want to save the whole session after open some files. So we first do "os.chdir(path)" to where we want to store the file. Then we use "rc("save current_session.py")" to save the current session info to a file. However, after we changed the current working directory correctly, "rc("save current_session.py")" still fails and displays error message of "Directory () does not exists". I have attached the code and error we encounter. I checked the current working directory right before calling "rc("save current_session.py)" and I am sure the current working directory is correct and is not (). Is there any settings we missed that result in rc(command) only execute at directory ()? Or is there any way that we can specify which directory we want to save the session using rc(command)? We tried it on 2 Mac but only one of them has this problem. I am thinking maybe some preference setup would cause this problem? Also, we encountered a problem of "Access Denied" when modifying the files from Chimera. On one Mac, we updated to the latest version chimera. But when we run our extension, we get "Access Denied" error when try to remove some files. No such error occurs within the same Mac before updating the version. Do you have any clue why that happens. If there is any question regarding our extension, please let me know! For more information about our lab, here is the link to our website: http://www.kiharalab.org/index.php. Kihara Bioinformatics Laboratory, Purdue University<http://www.kiharalab.org/index.php> www.kiharalab.org Area of Research Dr. Daisuke Kihara Principal Investigator. Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. Thank you in advance for your help and looking forward to your reply! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Summit supercompuer
by Victor Padilla-Sanchez 22 Jan '19

22 Jan '19

Dear Chimera, Would you tell me if someone has developed/ported Chimera to Summit supercomputer at Oak Ridge National Laboratory ? Please let me know, Thank you very much, Victor Padilla-Sanchez, PhD

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Auto-start extension in the Chimera
by Yuhong Zha 11 Jan '19

11 Jan '19

Dear Sir or Madam, This is Yuhong Zha from the Kihara Bioinformatics Laboratory. We are currently developing a Chimera extension to implement our MAINMAST algorithm. However, we encountered a problem of how to automatically start our extension when opening the Chimera. Now we have to go to IDLE and manually type "import our_extension.gui" to import our extension. Is there a way in the Chimera that could allow us to automatically open the extension every time we start the Chimera? Our current Chimera version is UCSF Chimera, production version 1.12 . If there is any question regarding our extension, please let me know! For more information about our lab, here is the link to our website: http://www.kiharalab.org/index.php. Kihara Bioinformatics Laboratory, Purdue University<http://www.kiharalab.org/index.php> www.kiharalab.org Area of Research Dr. Daisuke Kihara Principal Investigator. Our research interests lie in the area of bioinformatics. We employ computational methods to elucidate intertwined relationships between protein/gene sequences, structure, function, interactions, genome, and pathways. Thank you in advance for your help and looking forward to your reply! Best, Yuhong Zha, Kihara Bioinformatics Laboratory, Department of Biological & Computer Science at Purdue University

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Chimera orbitals alias question
by Benjamin Looker 16 Oct '18

16 Oct '18

Hello! My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function? An alias such as: alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. Any help would be greatly appreciated! Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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