Resetting $HOME won't work for me personally since I do have some custom
stuff in ~/.coot.py. I could symlink it to the coot home folder, of
course. Hopefully, no other problems pop up and coot does not rely on some
configuration file stored in the actual home folder.
Making .CCP4 folder unreadable is a better hack for sure - this way one
can't open CCP4 accidentally and overwrite the database.
Creating a separate account to just run coot (ideally configured to allow
su without a password) is another possibility.
None of this is ideal, of course. Adding option to coot preferences to
disable CCP4 folders is.
Probably the non-ugly one-way hack is to put return statement at the top of
add_ccp4i_projects_to_optionmenu in c-interface-gui.cc and compile from
source.
Cheers,
Ed.
---
Coot verendus est
On Thu, Nov 10, 2016 at 2:58 PM, Ethan A Merritt <merr...@u.washington.edu>
wrote:
> On Thursday, 10 November, 2016 14:01:01 Edwin Pozharski wrote:
> > This is an ugly hack, but here goes
>
> [...]
>
>
> Wouldn't it be cleaner to wrap coot in a script that either
> - resets $HOME to a directory that doesn't hold the .CCP4 folder
> - uses sgid + group permissions to prohibit read access to that directory
> - runs in a bind mount environment that does not contain .CCP4 or
> provides a minimal alternative file
>
>
> If you are using a bash shell, this can be as easy as invoking
> coot as:
>
> [1] HOME=/somewhere/else coot
>
>
> Ethan
>
> >
> > 1. Prior to opening coot, rename you .CCP4 folder. (bash: mv .CCP4
> > .CCP4_hidden)
> > 2. Open coot. Do what you need to do.
> > 3. Close coot.
> > 4. Restore .CCP4 folder (bash: mv .CCP4_hidden .CCP4)
> >
> > You can make a shortcut by putting this into your .bashrc
> >
> > coot_no_ccp4_folders ()
> > {
> > mv ~/.CCP4 ~/.CCP4_hidden
> > coot
> > mv ~/.CCP4_hidden ~/.CCP4
> > }
> >
> > Use with caution - if you mess up, you may lose all your CCP4
> configuration.
> >
> > This is not very convenient, since you cannot use ccp4 in the meantime -
> I
> > checked and the list of CCP4 folders does come up if you restore the CCP4
> > database folder while coot is still running. If you do use CCP4 in the
> > meantime, it will create an empty database, which is obviously not what
> you
> > want.
> >
> > If you are into hacking the coot source (with proper apologies to Paul),
> > then find src/graphics-info.cc file in your coot source, go to
> > ccp4_defs_file_name method and mess with it in an obvious way - it
> returns
> > the path to your CCP4 database folder, so just change it to something
> > non-existent. Compile custom coot binaries as usual and see what
> happens.
> > It might break spectacularly in case this method is used in a way other
> > than getting the CCP4 project folders listed in the file opening dialog.
> > Or it may behave exactly as you wish. Live dangerously :)
> >
> > My complaint about this feature is that it lists folder names, not
> project
> > names (I realize this might require customization of the dialog, so not
> > necessarily easy to fix). My habit is to create CCP4 projects as need
> and
> > name corresponding folders ccp4 inside another folder that holds the
> data.
> > As a result, I end up with a bunch of "ccp4" items in the list of
> folders,
> > which is unusable (I think it shows the full path if you hover over the
> > name, but that's not too helpful if you are looking for a particular
> > project. Of course, I should simply name folders in a more
> comprehensible
> > way.
> >
> > HTH,
> >
> > Ed.
> >
> > On Thu, Nov 10, 2016 at 12:30 PM, Gerhard Fischer <gf...@cam.ac.uk>
> wrote:
> >
> > > Dear all,
> > >
> > > I am having an issue with the "open file" dialogue in Coot:
> > >
> > > Apparently, there is some kind of connection between Coot and CCP4,
> which
> > > causes all the ccp4-project-directories to appear on the lefthand side
> > > under "places".
> > >
> > > Is there a way to avoid this - I have plenty of different
> CCP4-projects,
> > > many of them old, and I would like to use the space to manually link to
> > > relevant directories.
> > >
> > >
> > > I cannot manually remove these directories using the remove button
> (greyed
> > > out), and new directories can only be added manually to the very
> bottom of
> > > the list (and not moved up) - which is quite a way to scroll down, and
> not
> > > for quickly switching folders.
> > >
> > > I am on Kubuntu 16.04 LTS, but had this issue on openSUSE 13.2 as
> well. I
> > > have recently tried with Coot 0.8.7-pre (standalone) and 0.8.3
> (installed
> > > through CCP4).
> > > I can see the folders even when I start standalone coot and do not
> source
> > > CCP4.
> > >
> > > Any ideas?
> > >
> > >
> > > Best wishes,
> > >
> > > Gerhard
> > >
> > > --
> > > Gerhard Fischer, PhD
> > > Postdoctoral Research Associate
> > >
> > > University of Cambridge
> > > Department of Biochemistry
> > > 80 Tennis Court Road
> > > CB2 1GA Cambridge
> > > United Kingdom
> > >
> > > ---
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>
> --
> Ethan A Merritt
> Biomolecular Structure Center, K-428 Health Sciences Bldg
> MS 357742, University of Washington, Seattle 98195-7742
>
>
