[Chimera-users] Move molecule to center of rotation?

Tom Goddard goddard at sonic.net
Thu Oct 29 15:52:23 PDT 2015


Hi Oliver,

  Ok, in tonight’s daily build you can save

	move cofr model #3

to move model #3 so that its center is at the current center of rotation.

  Tom


> On Oct 28, 2015, at 12:33 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Match could work - matching a pseudo-atom at the center of rotation of the selected molecule to a pseudo atom at the current cofr would do the trick.
> 
> Move also works - if i measure the centers of rotation of two independent models I can match their positions by using move with the x,y,z offsets (after selecting/unselecting models for motion).
> 
> Syntax would be something like move_mol_here #model_id, no need for any extra flags that I can think of.
> 
> Thanks!
> 
> Oli.
>> On Oct 28, 2015, at 3:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Oliver,
>> 
>> Ok, you do a rotational search so all you need is to get the molecule close to where you want to fit it.  What you are asking for is more like the “match” command which aligns one molecule with another, than the “move” command which displaces a molecule by an offset from its current position.  But the match command won’t work because the center of rotation is not a molecule so you can’t align to it.  I’m more convinced of the need now, but I don’t see a good way to fit this in as an option to a current Chimera command.  Do you have a proposal for exactly the command syntax you want?
>> 
>> 	Tom
>> 
>> 
>> 
>>> On Oct 28, 2015, at 11:08 AM, Oliver Clarke  wrote:
>>> 
>>> Hi Tom - moving only one model is not a problem - i do that using "~select all" and "select n”, where n is the model id absent the hash, although your shortcuts look much more convenient.
>>> 
>>> It’s true that once you get the model to the right place, you need to reorient it - but I can do that automatically using something like "fitmap #2 #1 search 100 radius 5” if I know the model is roughly in the right place, whereas I would need to use a much larger radius if the model is further away.
>>> 
>>> Using the cofr marker you implemented, it is easy to get the cofr localized to a precise location in 3d space, and it would definitely be very useful to be able to move molecules to that location - I use similar functionality in Coot all the time. It’s not a necessity of course, but it would certainly make things faster.
>>> 
>>> Cheers,
>>> Oli.
>>>> On Oct 28, 2015, at 2:01 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>> 
>>>> Hi Oliver,
>>>> 
>>>> I’m not convinced that this will help fitting molecules in maps because once you get the molecule roughly in the right place, you still need to orient it to get it to fit.  So you still have the same problem that you somehow have to move only that model.  I typically do this with keyboard shortcut “ao” (activate only) which makes only the selected model movable.  I then put it where I want with the mouse and use shortcut “at” (activate toggle) or “aa” (activate all) which returns to all models moving.  Using “at” is particularly good because then hitting “at” again returns to just that same one model being movable (even if the selection has changed). Another approach is to use the “Movement Mouse Mode” tool (menu Tools / Movement) in “Move molecule” mode, then when you click and drag on any molecule it moves just that molecule.
>>>> 
>>>> At one time I had a keyboard shortcut that moved a selected model to the center of view that I used in cases where a model started out extremely far away.  But that is not in Chimera — I found it so rarely useful.
>>>> 
>>>> 	Tom
>>>> 
>>>> 
>>>> 
>>>>> On Oct 28, 2015, at 6:53 AM, Oliver Clarke wrote:
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other  models for motion and moving using the “move” command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation.  I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc.
>>>>> 
>>>>> Cheers,
>>>>> Oliver.
>>>>> _______________________________________________
>>>>> Chimera-users mailing list
>>>>> Chimera-users at cgl.ucsf.edu
>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>> 
>>>> 
>>> 
>>> 
>> 
> 
> 
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