@Ana: great idea to clean up the menus of Coot. It can indeed be difficult to hunt down the menu or dialog screen to find the feature that you need. (In MacOS, there is a neat feature where one can search all the menu items from the Help menu. Such a feature would be excellent for coot.)
@Oli: Thank you for your suggestion. I tried renaming that directory, but I still miss the “Refine” and “Morph” menu items. I also tried to copy the whole .coot-preferences directory over to the problematic mac, but that did not help either. Very annoying. Are there other ways to toggle on/off menu items? Regards, Daniel On 4 Sep 2019, at 13:07, Ana Casañal <[email protected]<mailto:[email protected]>> wrote: Hi all, The functions that were placed under ‘extensions’ are now located under tabs that relate to the type of operation to be performed. They are also organised in alphabetical order. The reason is that this way, all Coot functionalities can be found more easily. We have two new tutorials available for cryo-EM (also useful for crystallography), based on Coot 0.9. https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/Coot-Cryo-EM-basics.html https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/Coot-Cryo-EM.html All the best, Ana On 4 Sep 2019, at 11:37, Oliver Clarke <[email protected]<mailto:[email protected]>> wrote: Hi Daniel, Extensions is gone in 0.9-pre - the functions that used to be there have mostly been subsumed into other menus (mostly in Calculate if I recall correctly). As to what is different on your other macs, there are several menus (e.g. Refine, Morph, Glyco) that can be set to appear via a preference or the presence of a script in the ~/.coot-preferences dir - perhaps this is the case? Cheers Oli On September 4, 2019 at 6:35 GMT, Daniel Larsson <[email protected]<mailto:[email protected]>> wrote: Hi Oliver, Yes, that was a great tip, which Colin Palmer already suggested. This information should be more visible on the coot page. Now I ran into a funny (or not so funny) problem. On one of my macs with 0.9-pre several of the menus do not show up. I only get File, Edit, Calculate, Draw, Measures, Validate, About, Ligand. I miss e.g. Extensions! The most strange thing is that on my other mac I have many more menus. Anyone got a clue what happens? I used the exact same tar balls to install ccp4 and ccpem for both macs! Regards, Daniel On 4 Sep 2019, at 01:11, Oliver Clarke <[email protected]<mailto:[email protected]>> wrote: Hi Daniel - try downloading the latest nightly of CCP-EM (http://www.ccpem.ac.uk/download.php) - this includes a pre-built version of COOT 0.9-pre which mostly works fine on my Mac Cheers Oli On September 3, 2019 at 23:04 GMT, COOT automatic digest system <[email protected]<mailto:[email protected]>> wrote: There are 4 messages totaling 153 lines in this issue. Topics of the day: 1. Coot 0.9 pre-release on a mac? (3) 2. Problem with ProSMART restraints for RNA in 0.9-pre ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ---------------------------------------------------------------------- Date: Tue, 3 Sep 2019 08:40:11 +0000 From: Daniel Larsson <[email protected]<mailto:[email protected]>> Subject: Coot 0.9 pre-release on a mac? Hi all, I work on a mac and use the Scott Lab binaries. I currently use version 0.8.9.2-pre EL (revision count 7891). Watching Paul's introduction on YouTube (www.youtube.com/watch?v=hhB8qUBBnJQ<http://www.youtube.com/watch?v=hhB8qUBBnJQ>), It seems to be much snappier than 0.8.9 and have a lot of nice features, such as rotamer and ramachandran indicators. Anyone having luck with building the 0.9 beta (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/pre-releases/experimental/) on a mac or have binaries? I have High Sierra and use Homebrew for most libraries and commandline tools. 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 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ------------------------------ Date: Tue, 3 Sep 2019 10:37:21 +0000 From: Colin Palmer - UKRI STFC <[email protected]<mailto:[email protected]>> Subject: Re: Coot 0.9 pre-release on a mac? Hi Daniel, We compile Coot 0.9-pre for Mac as part of the CCP-EM suite. You can download it from here: http://www.ccpem.ac.uk/download.php The most up-to-date build of Coot is in the latest nightly release - scroll down the page to find it. Best wishes, Colin -----Original Message----- From: Mailing list for users of COOT Crystallographic Software <[email protected]<mailto:[email protected]>> On Behalf Of Daniel Larsson Sent: 03 September 2019 09:40 To: [email protected]<mailto:[email protected]> Subject: Coot 0.9 pre-release on a mac? Hi all, I work on a mac and use the Scott Lab binaries. I currently use version 0.8.9.2-pre EL (revision count 7891). Watching Paul's introduction on YouTube (www.youtube.com/watch?v=hhB8qUBBnJQ<http://www.youtube.com/watch?v=hhB8qUBBnJQ>), It seems to be much snappier than 0.8.9 and have a lot of nice features, such as rotamer and ramachandran indicators. Anyone having luck with building the 0.9 beta (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/pre-releases/experimental/) on a mac or have binaries? I have High Sierra and use Homebrew for most libraries and commandline tools. 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 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ------------------------------ Date: Tue, 3 Sep 2019 11:38:23 +0000 From: Daniel Larsson <[email protected]<mailto:[email protected]>> Subject: Re: Coot 0.9 pre-release on a mac? Hi Colin, That is a great suggestion! I will try that. Thanks a lot! Regards, Daniel > On 2019-09-03, at 12:37, Colin Palmer - UKRI STFC > <[email protected]<mailto:[email protected]>> wrote: > > Hi Daniel, > > We compile Coot 0.9-pre for Mac as part of the CCP-EM suite. You can download > it from here: http://www.ccpem.ac.uk/download.php > > The most up-to-date build of Coot is in the latest nightly release - scroll > down the page to find it. > > Best wishes, > Colin > > > -----Original Message----- > From: Mailing list for users of COOT Crystallographic Software > <[email protected]<mailto:[email protected]>> On Behalf Of Daniel Larsson > Sent: 03 September 2019 09:40 > To: [email protected]<mailto:[email protected]> > Subject: Coot 0.9 pre-release on a mac? > > Hi all, > > I work on a mac and use the Scott Lab binaries. I currently use version > 0.8.9.2-pre EL (revision count 7891). Watching Paul's introduction on YouTube > (www.youtube.com/watch?v=hhB8qUBBnJQ<http://www.youtube.com/watch?v=hhB8qUBBnJQ>), > It seems to be much snappier than 0.8.9 and have a lot of nice features, > such as rotamer and ramachandran indicators. Anyone having luck with building > the 0.9 beta > (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/pre-releases/experimental/) > on a mac or have binaries? I have High Sierra and use Homebrew for most > libraries and commandline tools. > > 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 > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ------------------------------ Date: Tue, 3 Sep 2019 13:47:48 +0000 From: Daniel Larsson <[email protected]<mailto:[email protected]>> Subject: Problem with ProSMART restraints for RNA in 0.9-pre Hi all, Now I got 0.9-pre working (thanks Colin Palmer for the suggestion!). In the new version, I have problem generating ProSMART restraints for RNA. It works fine for proteins. Anyone else experiencing the same problem and know how to solve it? I have also installed the latest version of CCP4. 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 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ------------------------------ End of COOT Digest - 27 Aug 2019 to 3 Sep 2019 (#2019-54) ********************************************************* ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ________________________________ To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ________________________________ To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ________________________________ To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
