[Chimera-users] Center of rotation cross-hair

[Oliver Clarke]

In case it is useful to anyone else, the solution I found to this was to
create an alias as follows:

alias ^cofron set showcofr; cofr view; clip on

and then use this command whenever I load a new structure or map. This
seems to work quite well and allows for easy navigation around structures.

Cheers,
Oliver.

On Wed, Jun 24, 2015 at 3:31 PM, Tom Goddard <goddard at sonic.net> wrote:

> Unfortunately I see no easy solution to improve center of view rotation
> mode.  Adding a preference to keep clipping enabled would not be too hard —
> but Chimera C++ code always turns the clipping off when the first model is
> opened.  That is in a C++ routine (viewAll) that is called from many places
> so I can’t change it without breaking or fixing other code.  Another option
> is to keep the depth of the center of rotation fixed even while the clip
> planes are moving.  Again this change could break lots of code.  We are
> working on Chimera 2 now, and this problem has a very easy if tedious
> solution — manually enable clipping after you open a model.  So I don’t see
> it being fixed in Chimera 1.
>
> Tom
>
>
> On Jun 23, 2015, at 11:22 AM, Oliver Clarke  wrote:
>
> Yes Tom that is exactly right - don’t really mind how it works so long as
> center of view rotation works (I guess that is for Chimera 2 though). In
> the meantime a preference for clip planes on as you describe would be great!
>
> Cheers,
> Oliver.
>
> On Jun 23, 2015, at 1:56 PM, Tom Goddard  wrote:
>
> Hi Oliver,
>
>   Is the main point of your request to be able to set a clip plane on/off
> preference so that center-of-view rotation works?  If so the what is needed
> is to fix center-of-view rotation.  I made a bug report for that problem
> yesterday.
>
> http://plato.cgl.ucsf.edu/trac/chimera/ticket/14028
>
> With clip planes enabled they still need to automatically adjust. For
> instance before you open the first data set they are positioned at z -1 and
> 1.  If they don’t adjust when you open the first data you won’t see the
> data.  Commands like “focus” with no arguments are documented to turn off
> clip planes.  If you want clip planes to remain enabled you would use
> “focus #0”.  We won’t add global setting that override the documented
> behavior of commands.  Still it probably is possible to make clip planes on
> a preference with the planes adjusting when the first data set is opened.
> This is the way Chimera behaved 5 years ago.
>
> Tom
>
>
> On Jun 23, 2015, at 6:39 AM, Oliver Clarke  wrote:
>
> Dear Tom - just tried this out and it works exactly as I would hope - this
> makes it much easier to navigate precisely within a structure, thank you.
>
> One additional request on this - would it be possible to add a parameter
> that locks global clipping on for the session unless explicitly altered by
> the user?
>
> At the moment, it seems that global clipping is off by default for a new
> session even if I try to save it in the camera settings, and then in
> “center of view” mode the cofr keeps shifting about as the clipping planes
> auto adjust. It would be great to have a way to set clipping planes on as
> the default unless explicitly altered.
>
> Best,
> Oliver.
>
>
> On Jun 22, 2015, at 7:58 PM, Tom Goddard wrote:
>
> Hi Oliver,
>
> I added display of a cross hair (plus sign) at the center of rotation in
> the graphics window.  You turn it on with command
>
> set showCofR
>
> and turn it off with
>
> ~set showCofR
>
> The crosshair is white on black (and dark) backgrounds and black on white
> (or light) backgrounds.  This will be in tonight’s daily build.
>
> Tom
>
>
>
>
>
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>
>
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