> The only difficulty I have with these movements is that when
> you do fragment rotation you never know exactly what the axis
> of rotation is going to be. Usually I have to play around
> with the overall camera view and the atoms I'm grabbing a few
> times before I can get the rotation I want.
I have received some good suggestions about how to deal with this, by having
PyMOL automatically set the origin at the fragments center of mass. In the
meantime, ctrl-shift-middle-click to set the origin on a particular atom
before commencing to rotate.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080
. Biz:(650)-872-0942 Tech:(650)-872-0834
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. mailto:warren@...
> -----Original Message-----
> From: pymol-users-owner@...
> [mailto:pymol-users-owner@...] On Behalf Of
> Al_Pierce@...
> Sent: Thursday, February 17, 2005 8:56 AM
> To: Sri Krishna Subramanian
> Cc: PyMOL-users@...;
> pymol-users-admin@...
> Subject: Re: [PyMOL] Re: align proteins in pymol
>
> If you set the mouse mode to 3-button editing mode, you'll
> see that Shift-Left and Shift-Middle are RotF and MovF, respectively.
>
> So with nothing selected, if you do Shift-Left, grab an atom
> of a molecule and move it, the whole molecule will rotate
> while all other structures are fixed. The same process with
> Shift-Middle will translate that molecule only.
>
> If you only want to move part of a molecule, you can
> basically break the molecule into 2 separate fragments with
> Ctrl-Middle selections. Then when you do a rotation or
> translation only the end of the molecule you grabbed will move.
>
> The only difficulty I have with these movements is that when
> you do fragment rotation you never know exactly what the axis
> of rotation is going to be. Usually I have to play around
> with the overall camera view and the atoms I'm grabbing a few
> times before I can get the rotation I want.
>
>
>
> Sri Krishna Subramanian <krishna@...> Sent by:
> pymol-users-admin@...
> 02/17/2005 11:35 AM
>
> To
>
> cc
> <PyMOL-users@...>
> Subject
> [PyMOL] Re: align proteins in pymol
>
>
>
>
>
>
> Dear Torin,
> Thanks for your reply. However my question
> was not about automatic alignment of two protein structures.
> I want to move one of the structures while keeping the other
> one fixed, so that I can consider alternate alignments etc ..
> So is there a way to do that with PyMOL.
> thanks
> krishna
>
> > align prot1////ca,prot2////ca >
> > prot1 will then be superimposed onto prot2
> >
> > your two proteins will obviously require some degree of homology.
> >
> > Best,
> > Torin
> >
> >
> >
>
>
>
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