Oh, I hadn’t thought of trying that, that works! Obviously it would still be great if this issue was fixed (I guess it’s MacOS rather than PyMOL that’s to blame here), but this is a decent workaround.
Thanks! /Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Nicholas Clark <ndcla...@buffalo.edu> Reply-To: Nicholas Clark <ndcla...@buffalo.edu> Date: Monday, February 6, 2023 at 12:46 To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 ---------- Forwarded message --------- From: Nicholas Clark <ndcla...@buffalo.edu<mailto:ndcla...@buffalo.edu>> Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 To: Julia Griese <julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>> Julia, I have the same issue with PyMOL. After it opens the blank session, if you return to the file explorer and try to reopen the file it will open the session correctly. Seems what you’re trying to open gets “lost” while loading PyMOL. Best, Nick Clark On Mon, Feb 6, 2023 at 5:38 AM Julia Griese <julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>> wrote: Hi all, I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my computer’s nagging) and am now encountering some issues with Coot and PyMOL. The issues persist after updating to version 13.2. Regarding Coot version 0.9.8.7<http://0.9.8.7>: The rotate/translate zone function does not work properly. Everything works when using the slider bars in the dialog, and translating with the mouse works, but rotating with the mouse does not work. The region to be rotated disappears from view. I can make do with the slider bars, but feel that I have much better fine control and it’s much faster when using the mouse to rotate. Has anyone else encountered this problem and knows of a workaround? (I’m aware of the workaround for the main window disappearing when you delete items.) Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to open any kind of file that is set to open in PyMOL by default (pdb or cif coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL files through the File Open dialog, having to navigate through the entire folder structure first, which obviously takes much longer. Has anyone else encountered this issue and knows how to fix it? Best, Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se> phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.se%2Fstructural-biology%2Fgriese-lab%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C20d5eb5f89124f88131408db082e3833%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638112766972241444%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8bFzv1MlDG9wxZdBaPgnYX%2BkF%2BrK7TKr%2FGivROK3hXE%3D&reserved=0> 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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C20d5eb5f89124f88131408db082e3833%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638112766972241444%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4GAZj1fdgo%2FO7UnQFPgkfnefTajRC%2FTR4TZM2S1ZEd0%3D&reserved=0> -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
