## [PyMOL] Transformation Matrices

 [PyMOL] Transformation Matrices From: Jacob Keller - 2011-12-29 17:33:21 ```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 -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-keller2@... ******************************************* ```

 [PyMOL] Transformation Matrices From: Jacob Keller - 2011-12-29 17:33:21 ```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 -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-keller2@... ******************************************* ```
 Re: [PyMOL] Transformation Matrices From: Thomas Holder - 2011-12-29 20:33:05 ```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 ```
 Re: [PyMOL] Transformation Matrices From: Jason Vertrees - 2012-01-03 03:38:50 ```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 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 (PyMOL-users@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```
 Re: [PyMOL] Transformation Matrices From: Jacob Keller - 2012-01-03 18:11:34 ```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 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 > 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 (PyMOL-users@...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@... > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jason.Vertrees@... > (o) +1 (603) 374-7120 -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-keller2@... ******************************************* ```
 Re: [PyMOL] Transformation Matrices From: Jason Vertrees - 2012-01-03 18:43:23 ```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 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 > 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 >> 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 (PyMOL-users@...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@... >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jason.Vertrees@... >> (o) +1 (603) 374-7120 > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-keller2@... > ******************************************* -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```