Jacob, Thomas Holder apprised me of a detail that effected the cealign code (I used transform_selection instead of transform_object). This code has been updated in the open-source repository; matrix_copy should now work after aligning with cealign.
Cheers, -- Jason On Tue, Jan 3, 2012 at 1:11 PM, Jacob Keller <[email protected]> wrote: > Hi Jason, > > thanks for calling my attention to this--this is very good to know (I > looked up the camera/model space idea as well--very helpful)! > > Jacob > > On Mon, Jan 2, 2012 at 9:38 PM, Jason Vertrees > <[email protected]> wrote: >> Jacob, >> >> The easiest will be to use matrix_copy. All objects start out with >> their object matrix set to the identity. One you drag them around or >> move them through an alignment, their matrices change. You can then >> easily copy one object's matrix onto another object. >> >> Cheers, >> >> -- Jason >> >> On Thu, Dec 29, 2011 at 3:32 PM, Thomas Holder >> <[email protected]> wrote: >>> Hi Jacob, >>> >>> regarding "alignto" and states' iter-relations, this has recently been >>> fixed in open-source pymol. >>> >>> "align" and "super" both take arguments "mobile_state" and >>> "target_state" and also preserve states' iter-relations. >>> >>> Example: >>> align 1d7q, 2oqk, mobile_state=7, target_state=1 >>> >>> The matrix you get like this: >>> print cmd.get_object_matrix('1d7q') >>> >>> You can use this matrix with "transform_selection". >>> >>> There is also "matrix_copy" command, but I haven't tried it with >>> multi-state stuff. >>> >>> http://pymolwiki.org/index.php/Align >>> http://pymolwiki.org/index.php/Get_object_matrix >>> http://pymolwiki.org/index.php/Transform_selection >>> http://pymolwiki.org/index.php/Matrix_Copy >>> >>> Cheers, >>> Thomas >>> >>> Jacob Keller wrote, On 12/29/11 18:33: >>>> Dear List, >>>> >>>> I want to superpose a series of 30 states on another (single-state) >>>> model in the following way: >>>> >>>> --Superpose the best (closest-fitting) state first. (I know which one this >>>> is) >>>> --Output that transformation matrix >>>> --Transform other states by same matrix to preserve states' inter-relation. >>>> >>>> Is there some function that will output such a matrix, for input into, >>>> say, "transform_selection"? >>>> >>>> I have done this using the alignto command, but it ruins the states' >>>> interelations. >>>> >>>> Jacob >>> >>> -- >>> Thomas Holder >>> MPI for Developmental Biology >>> Spemannstr. 35 >>> D-72076 Tübingen >>> >>> ------------------------------------------------------------------------------ >>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex >>> infrastructure or vast IT resources to deliver seamless, secure access to >>> virtual desktops. With this all-in-one solution, easily deploy virtual >>> desktops for less than the cost of PCs and save 60% on VDI infrastructure >>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox >>> _______________________________________________ >>> PyMOL-users mailing list ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: [email protected] > ******************************************* -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
