February 2020 - Chimera-users - RBVI Mailing Lists

(no subject)
by Thirumurugan Prakasam 29 Oct '21

29 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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visualizing potential with volume data
by Christos Deligkaris 06 Mar '20

06 Mar '20

dear all, I have obtained a cube file from NWChem with the electrostatic potential around a molecule. I visualized the molecular surface using Actions->Surface->Show and then colored it using the volume data (followed instructions https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in tools->surface color (electrostatic surface coloring)) . Since I do not have my data stored in a potential file, can I still do the surface offset? The chimera tool webpage discusses why that is preferred than showing the potential on the solvent excluded surface and it seems to me that option to not be available with volume data. Also, my surface does not look like the electrostatic potential surface shown here: https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html . The molecular surface we get with Action->Surface->Show seems to be constructed with greater atomic radii than the one shown in that image. I am not sure how important that is though. Is there a way to ask Chimera to visualize the electrostatic potential volume data with the same options Chimera would use if it was reading a Delphi, PBS file? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics

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Auto-Stereo 3D
by Engelhardt, Peter 28 Feb '20

28 Feb '20

Dear Chimera developers, We are most interested of always using stereo in Chimera. Lately there have been presented Auto-Stereo 3D displays: https://www.tri-evolution.com/en/auto-stereo-3d/ Auto-Stereo 3D - TRI Evolution – 3D without glasses<https://www.tri-evolution.com/en/auto-stereo-3d/> We unfold digital vision. We unfold your product and video data in “GLASSES-FREE 3D”. We offer numerous services and solutions for perfect handling of the latest auto stereo 3D technology. We are an official Solutions Partner of 3D Global. Find out everything worth knowing about our AS3D offer in this section. AS3D Hardware AS3D Hardware More […] www.tri-evolution.com Because of this convenience in 'no need to use any stereo glasses' we wonder if Chimera is supporting Auto-stereo 3D displays, now or in near future. We thank you in advance Cheers Peter

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Comparison of cryo-em maps
by Dmitry Semchonok 28 Feb '20

28 Feb '20

Dear colleagues, I have similar cryo-em maps that have also some differences. I want to compare them. Is there a tool in chimera that can compare the cryo-em maps? Thank you! Sincerely, Dmitry

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debug
by 陈文心 27 Feb '20

27 Feb '20

When I open chimera, introduction webpages will continuously open and many interfaces pop out. Could you please help me solve the problem? Thanks a lot. 发送自 Windows 10 版邮件应用

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Contour plot of intersurf surface
by Miguel Romero 27 Feb '20

27 Feb '20

Hello, I am looking for a way to generate a contour plot from the interface surface generated with the intersurf command. The idea is to have a 2D representation of the interface. I would really appreciate any suggestion. Thanks in advance, Miguel

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Ctrl-Shift-click iimpaired on MacOS Mojave
by Visvaldas K. 27 Feb '20

27 Feb '20

Dear Chimera Users, recently I noticed a bug (?): I am not able to multiple select atoms using Ctrl-Shift-click easily, as I was able before (I am not sure when the problem started). If I use mouse, sometimes I am able to select two atoms after a while by going back and forth between the two atoms and keep clicking, and after some time I succeed to select, but but the required number of tries is unpredictable. However, with the touchpad, forget it, it does not work at all. Needless to say, I find this to be very annoying. I tried today's Chimera daily build, versions 14 and 13.1 with the same results. I am running MacOS Mojave. Sincerely yours, Visvaldas

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How to change font size for scale bar
by Engelhardt, Peter 27 Feb '20

27 Feb '20

Hi We can’t find any options for font size in scale bar wondering if possible. Any suggestions Cheers Peter Sent from my iPhone

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Unable to Install ChimeraX 1.14 on MacOS 10.15.3
by Shawn Rumrill 26 Feb '20

26 Feb '20

Hello, I recently tried installing ChimeraX 1.14 on my MacBook Pro OS 10.15.3. I receive a message that the software cannot be installed because it cannot be verified and needs to be updated. So you have any solution to this problem? Screenshot of error message attached. Best, Shawn Rumrill srr131(a)cabm.rutgers.edu<mailto:srr131@cabm.rutgers.edu> [cid:F2EDAD80-53DE-442C-B590-72AD2EE15870@ruw.rutgers.edu]

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Chimera-users February 2020