- Chimera-users - RBVI Mailing Lists

Change default pseudobond color?
by Oliver Clarke 10 Mar '20

10 Mar '20

Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli

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Numbers(markers) inside/on the map
by Dmitry A. Semchonok 10 Mar '20

10 Mar '20

Dear colleagues, I would like to place the numbers (markers) inside/on our map. Could you please prompt how to do that ? Thank you. Sincerely, Dmitry

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Regarding Structure minimize
by Yash Bahl 08 Mar '20

08 Mar '20

To do structure minmization, what is the adequate values? Steepest descent should be changed to 75 from 100. What else? Should intervals be also changed to 25? Thanks

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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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move labels
by Dieter Blaas 06 Mar '20

06 Mar '20

Hi, I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse? Thank you very much, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Choosing Help->Search Documentation causes seg fault
by Hua tiger 05 Mar '20

05 Mar '20

Hello, First of all thank you for your good work and assistance. Core dump trace is attached and a snippet follows. Choosing Help->Search Documentation causes seg fault. The remaining help menu items work fine. Please see below. Thank you so much. John ------------------------------------------------------------------- huatiger@huatiger:debug$ coredumpctl debug PID: 23503 (python2.7) UID: 1000 (huatiger) GID: 1000 (huatiger) Signal: 11 (SEGV) Timestamp: Sat 2020-02-29 14:35:13 EST (1min 8s ago) Command Line: /opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.py --debug Executable: /opt/UCSF/Chimera64-1.14/bin/python2.7 ... Core was generated by `/opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.'. Program terminated with signal SIGSEGV, Segmentation fault. #0 0x00007fe3a31c51f8 in uncompress2 () from /lib/x86_64-linux-gnu/libz.so.1 ---------------------------------------------------------------------------------------- huatiger@huatiger:Downloads$ cat /etc/os-release NAME="Ubuntu" VERSION="19.10 (Eoan Ermine)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 19.10" VERSION_ID="19.10" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL=" https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=eoan UBUNTU_CODENAME=eoan huatiger@huatiger:Downloads$ uname -a Linux huatiger 5.3.0-40-generic #32-Ubu

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LINK record not honoured in Chimera?
by Kate Kim 04 Mar '20

04 Mar '20

Hello, I would like to visualize a thioester bond between a CYS residue of my protein and a carbonyl carbon of ligand (DCR) in my model. I have a LINK record for the DCR-CYS thioester bond created from Jligand and inserted in the PDB right before the CRYST1 line. However, when I open this PDB in Chimera, the thioester linkage is not drawn. The distance between the C1 of DCR and SG of CYS is 1.79 angstrom. Does Chimera need something else other than the LINK record in the PDB to display the bond? Thank you, Kate

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desktop hardware
by joe viterbo 04 Mar '20

04 Mar '20

Hi everyone, I am about to purchase a PC desktop computer to run Chimera. Regarding the hardware, should I focus more on CPU speed & cores or should I focus more on a powerful GPU? Or should I try to find both? Thanks for your time! Best, Joe

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how to create a sphere in Chimera
by Ke Shyue-Chu 04 Mar '20

04 Mar '20

Hi, I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. Thank you. Sc Ke Professor Department of Physics National Dong Hua University Hualien, Taiwan

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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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