December 2020 - ChimeraX-users - RBVI Mailing Lists

Superimpose overall structure
by Zheng, Fengwei 11 Dec '20

11 Dec '20

Dear ChimeraX developers, Thank a bunch for developing this so gracious and powerful software for our community! May I ask how to superimpose the overall structures of two analogues? e.g., the E. coli sliding clamp beta is a ring-shaped homodimer (two chains), while the yeast sliding clamp PCNA is a ring-shaped homotrimer (three chains), and their overall structures are quite similar, but when I use the matchmaker to superimpose them, it seems always only use the chain A, but not the all chains, pls see figures below~ Stay safe and warm, Many thanks! [cid:d0647b0e-e6db-459b-9f0b-72ee21eb06c7] Best, Fengwei

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Saving models in ChimeraX
by Moradkhan, Tiglath A 10 Dec '20

10 Dec '20

Hi I have a question about saving homology models in ChimeraX. Does the save command allow saving homology models as pdb files? If so then how is it possible to specify which folder to save homology models? Thanks Tiglath

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Handling gltf file
by Suzanne Duce (Staff) 10 Dec '20

10 Dec '20

Hi, When I import a .glb gltf file that I generated in ChimeraX into Blender to reduce its file size. The colouring seems to be lost. Is there a way to reduce the .glb file size in ChimeraX (or using another program)? Or not to lose the colours when importing it into Blender? Regards, Suzanne The University of Dundee is a registered Scottish Charity, No: SC015096

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Change AltGr
by Daniel Esteban Palma Igor 09 Dec '20

09 Dec '20

Hi, pressing AltGr takes the cursor to the command line, is there any way to change this key? I can't write some characters when the ipython shell is docked. Regards, Daniel Palma Igor

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Move model from position
by Lara Koehler 09 Dec '20

09 Dec '20

Dear chimeras users and developers, I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position. Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar Lara KOEHLER Laboratoire de Physique Théorique et Modèles Statistiques Bureau L123 - Bâtiment 530 - Rue André Rivière 91400 Orsay [ http://www.universite-paris-saclay.fr/ | www.universite-paris-saclay.fr ]

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multiple isosurfaces for one map
by Daniel Larsson 07 Dec '20

07 Dec '20

Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Plugin developers switch from PyQt5 to PySide2
by Tom Goddard 02 Dec '20

02 Dec '20

For those who develop ChimeraX plugins with graphical user interfaces, today we switched ChimeraX from using PyQt5 to using PySide2. These are nearly identical Python interfaces to the Qt window toolkit. In your code you will probably only need to change imports of PyQt5 to instead import PySide2. There are a few other small differences (e.g. pyqtSignal becomes Signal, and QAction callbacks may not have the same arguments) and more details about the differences are in this ChimeraX ticket <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635#comment:34>https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635> We made the switch because PySide2 has a bigger community development team, part of the Qt project, and has less restrictive licensing. Tom

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Add Chain to AtomicStructure
by Daniel Esteban Palma Igor 02 Dec '20

02 Dec '20

Hi, is there a way to add a Chain object to an AtomicStructure? Regards, Daniel Palma Igor

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BUG - NotADirectoryError when start Chimerax
by 江文宏 01 Dec '20

01 Dec '20

Hi, I am a phD from Peking University, Beijing, China. And I downloaded the latest version(1.1) of Chimerax for Centos. And I installed the chimerax in the linux (centos7) by yum install ucsf-chimerax-1.1-1.el7.x86_64. And everything went well for the install/compiling process. However, when I started the chimerax in the terminal, the terminal returned this error: Do you have any idea about such errors? I also tried the older version(1.0), but I got the same error. BTW, I used python3.8. Thanks! All the best, Wenhong Jiang

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ChimeraX-users December 2020