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Hi Paul and Huw, Thanks for your emails. >That is all I get in the terminal too (Coot 0.8.1-pre rev 5423 on OS X 10.9.5) but the table of >"Questionable Waters" does appear (hidden underneath the main window). Is that not >happening for you? X11 window handling (especially with several applications using X11 open >across multiple desktops) does seem to be pretty unpredictable on OS X. Yes, thank you! I checked again and I actually get the "(command-in-path-or-absolute? *probe-command*)" message every time I just click the 'Validate' menu. And the questionable waters table is there, just hidden behind my main window (as you described). I did not see that before, because I am using an external screen and there the Coot window cannot be moved, just resized. When I disconnect the external screen, I can move the Coot window on my Mac's screen and find the waters table. So my question is: Any advice how to improve working with X11 on Mac? With Linux, you can find overlapping windows easily. X11 on Mac just gives one window per application, so any pop-up windows cannot be selected directly with the 'Window' menu. I will post this to the ccp4bb, too, with some other issues about X11. Thanks, Tobias. On Thu, Nov 20, 2014 at 1:00 AM, COOT automatic digest system < [log in to unmask]> wrote: > There are 7 messages totaling 362 lines in this issue. > > Topics of the day: > > 1. pdb info - where? (4) > 2. problems with validate waters (3) > > ---------------------------------------------------------------------- > > Date: Wed, 19 Nov 2014 05:26:51 +0000 > From: Frank von Delft <[log in to unmask]> > Subject: pdb info - where? > > Hi all - does coot have a way to let me see the pdb header? > > (Yes, I know I can open a text browser - but that's typically about 20 > clicks, especially if I pulled the coordinates directly from the PDB.) > > Specifically, where can I see cell and symmetry info? Apart from > scrolling through the console window? > > phx > > ------------------------------ > > Date: Wed, 19 Nov 2014 13:55:10 +0800 > From: Paul Emsley <[log in to unmask]> > Subject: Re: pdb info - where? > > On 19/11/14 13:26, Frank von Delft wrote: > > Hi all - does coot have a way to let me see the pdb header? > > There is a remarks browser under "About" > > > > (Yes, I know I can open a text browser - but that's typically about 20 > > clicks, especially if I pulled the coordinates directly from the PDB.) > > > > Specifically, where can I see cell and symmetry info? Apart from > > scrolling through the console window? > > Maps you can find using "Display Manager" -> Properties > > I don't recall if there is a way to similarly see model info of the top > of my head. > > Paul. > > ------------------------------ > > Date: Wed, 19 Nov 2014 12:25:22 +0100 > From: Tim Gruene <[log in to unmask]> > Subject: Re: pdb info - where? > > Hi Paul, > > Didn't know about the 'REMARKS' browser, very useful. > It would be a nice feature to have an info about the cell and symmetry > as Frank suggests. > > Cheers, > Tim > > On 11/19/2014 06:55 AM, Paul Emsley wrote: > > On 19/11/14 13:26, Frank von Delft wrote: > >> Hi all - does coot have a way to let me see the pdb header? > > > > There is a remarks browser under "About" > >> > >> (Yes, I know I can open a text browser - but that's typically about 20 > >> clicks, especially if I pulled the coordinates directly from the PDB.) > >> > >> Specifically, where can I see cell and symmetry info? Apart from > >> scrolling through the console window? > > > > Maps you can find using "Display Manager" -> Properties > > > > I don't recall if there is a way to similarly see model info of the top > > of my head. > > > > Paul. > > > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > ------------------------------ > > Date: Wed, 19 Nov 2014 13:22:51 +0100 > From: Tobias Beck <[log in to unmask]> > Subject: problems with validate waters > > Hi all, > > I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like to > validate waters. However, after selecting the criteria and hitting 'Ok', > the terminal only gives me > > (command-in-path-or-absolute? *probe-command*) > > Interestingly, all the other validation tools that I tested seem to work > find, including showing the Probe clashes... so Probe can be found and > seems to work? > > In the Scheme scripting window, executing > > > (command-in-path? *probe-command*) > > > gives me > > #t > > Any suggestions? I previously used an earlier Coot version (0.7?). This > also gave me the error describe above; that is why I tried the recent Coot > version, with no luck. > > Thank you in advance, > > Tobias. > > ------------------------------ > > Date: Wed, 19 Nov 2014 12:55:42 +0000 > From: Mark Brooks <[log in to unmask]> > Subject: Re: pdb info - where? > > It would be nice to have a widget like the ViewHKL cell and symmetry > widget, but that would be a nice to have. What a great program that is as > well (as Coot). > > A simple GtkTextView widget would be nice still if that's big enough etc. > > Mark > > On 19 November 2014 11:25, Tim Gruene <[log in to unmask]> wrote: > > > Hi Paul, > > > > Didn't know about the 'REMARKS' browser, very useful. > > It would be a nice feature to have an info about the cell and symmetry > > as Frank suggests. > > > > Cheers, > > Tim > > > > On 11/19/2014 06:55 AM, Paul Emsley wrote: > > > On 19/11/14 13:26, Frank von Delft wrote: > > >> Hi all - does coot have a way to let me see the pdb header? > > > > > > There is a remarks browser under "About" > > >> > > >> (Yes, I know I can open a text browser - but that's typically about 20 > > >> clicks, especially if I pulled the coordinates directly from the PDB.) > > >> > > >> Specifically, where can I see cell and symmetry info? Apart from > > >> scrolling through the console window? > > > > > > Maps you can find using "Display Manager" -> Properties > > > > > > I don't recall if there is a way to similarly see model info of the top > > > of my head. > > > > > > Paul. > > > > > > > -- > > Dr Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > > > > > ------------------------------ > > Date: Wed, 19 Nov 2014 21:13:55 +0800 > From: Paul Emsley <[log in to unmask]> > Subject: Re: problems with validate waters > > On 19/11/14 20:22, Tobias Beck wrote: > > Hi all, > > > > I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like > > to validate waters. However, after selecting the criteria and hitting > > 'Ok', the terminal only gives me > > > > (command-in-path-or-absolute? *probe-command*) > > > > Interestingly, all the other validation tools that I tested seem to > > work find, including showing the Probe clashes... so Probe can be > > found and seems to work? > > > > In the Scheme scripting window, executing > > > > (command-in-path? *probe-command*) > > > > gives me > > > > #t > > > > Hmm... That's strange. The Check/Delete water function is not dependent > on probe and reduce (I certainly don't get these messages). > > Also, I thought that the scheme scripting window in Coot for Mac had > been deactivated (for the moment) - so I don't know what is going on > there either. > > Paul. > > ------------------------------ > > Date: Wed, 19 Nov 2014 15:02:49 +0000 > From: Huw Jenkins <[log in to unmask]> > Subject: Re: problems with validate waters > > On 19 Nov 2014, at 12:22, Tobias Beck <[log in to unmask]> wrote: > > > I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like to > validate waters. However, after selecting the criteria and hitting 'Ok', > the terminal only gives me > > > > (command-in-path-or-absolute? *probe-command*) > > That is all I get in the terminal too (Coot 0.8.1-pre rev 5423 on OS X > 10.9.5) but the table of "Questionable Waters" does appear (hidden > underneath the main window). Is that not happening for you? X11 window > handling (especially with several applications using X11 open across > multiple desktops) does seem to be pretty unpredictable on OS X. > > > Huw > > ------------------------------ > > End of COOT Digest - 17 Nov 2014 to 19 Nov 2014 (#2014-5) > ********************************************************* > -- ___________________________________________ Dr. Tobias Beck - group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 fax: +49-241-80-99003 web: http://www.protein.ethz.ch/people/tobias ___________________________________________