[Chimera-users] Center of rotation cross-hair

Oliver Clarke olibclarke at gmail.com
Tue Jul 28 14:58:12 PDT 2015


Fantastic! Thanks Tom!

And thanks for answering my query regarding resampling, I had no idea that option existed.

Cheers,
Oliver.
> On Jul 28, 2015, at 3:03 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Oliver,
> 
>   Ok, I’ve added a clip command option “fromCenter true” that positions the plane relative to the center of rotation instead of relative to the current position.  For example,
> 
> 	clip hither 15 fromCenter true
> 
> positions the near plane 15 Angstroms in front of the center of rotation.  Positive values are towards the viewer and negative away for both near and far planes.  Will be in tonight’s daily build. Thanks for the suggestion.
> 
> 	Tom
> 
> 
>> On Jul 28, 2015, at 7:09 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>> 
>> Hi all,
>> 
>> With regards to this (and thank you very much Tom for the center of rotation crosshair, it makes navigating large maps much more enjoyable!), I have one more request pertaining to the same use case. 
>> 
>> Would it be possible at some point to add a way to adjust the clipping planes symmetrically about the center of rotation, in absolute rather than relative terms? E.g to set hither and yon clipping planes 15 Å either side of the cofr. 
>> 
>> I can adjust these symmetrically in relative terms by using an alias at the moment (alias ^symclip cofron; clip hither -$1; clip yon $1 - so symclip 10 shows the cofr crosshair, centers the cofr between the clipping planes and moves both hither and yon towards the cofr by 10 Å), but it would be more convenient to set the clipping window directly. 
>> 
>> The use case for this occurs when the user is navigating around a large map comprised of smaller domains, and wishes to focus in on a single domain (located at/near the center of rotation). Being able to clip an arbitrary distance either side of the COFR would be handy in this instance.
>> 
>> Cheers,
>> 
>> Oliver.
>>> On Jul 1, 2015, at 3:14 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
>>> 
>>> 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 <mailto: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 <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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