Print

Print
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
___________________________________________