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From: Lu L. <ll...@cs...> - 2008-01-25 12:27:59
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Hi all, Anyone know which algorithm PyMOL uses to align or super of two structures? Thanks a lot! Best, Linda |
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From: DeLano S. <de...@de...> - 2008-01-25 18:02:40
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Linda, It is not a published algorithm except in the sense that the implementation is open-source. In a nutsheel: "align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance). "super" does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of Lu Lin > Sent: Friday, January 25, 2008 4:29 AM > To: pym...@li... > Subject: [PyMOL] algorithm for alignment > > Hi all, > > Anyone know which algorithm PyMOL uses to align or super of > two structures? > > Thanks a lot! > > Best, > Linda > > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Lu L. <ll...@cs...> - 2008-01-26 06:39:03
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Dear Warren, Thank you for your reply! Besides, sometimes when I align two structures by their ca atoms, one of them keeps trembling, do you know why? Thanks again! Best regards, Linda DeLano Scientific wrote: > Linda, > > It is not a published algorithm except in the sense that the implementation > is open-source. In a nutsheel: > > "align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence > alignment followed by a series of refinement cycles intended to improve the > fit by eliminating pairing with high relative variability (e.g. >2 standard > deviations from the cycle's mean deviance). > > "super" does a sequence-independent structure-based dynamic programming > alignment followed by that same 3D refinement strategy. > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:de...@de... > > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of Lu Lin >> Sent: Friday, January 25, 2008 4:29 AM >> To: pym...@li... >> Subject: [PyMOL] algorithm for alignment >> >> Hi all, >> >> Anyone know which algorithm PyMOL uses to align or super of >> two structures? >> >> Thanks a lot! >> >> Best, >> Linda >> >> >> >> -------------------------------------------------------------- >> ----------- >> This SF.net email is sponsored by: Microsoft Defy all >> challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > |
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From: Lu L. <ll...@cs...> - 2008-01-27 03:44:27
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Dear Warren, Does the algorithm support flexible alignment? Thanks a lot! Best regards, Linda DeLano Scientific wrote: > Linda, > > It is not a published algorithm except in the sense that the implementation > is open-source. In a nutsheel: > > "align" does a BLAST-like BLOSUM62-weighted dynamic programming sequence > alignment followed by a series of refinement cycles intended to improve the > fit by eliminating pairing with high relative variability (e.g. >2 standard > deviations from the cycle's mean deviance). > > "super" does a sequence-independent structure-based dynamic programming > alignment followed by that same 3D refinement strategy. > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:de...@de... > > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of Lu Lin >> Sent: Friday, January 25, 2008 4:29 AM >> To: pym...@li... >> Subject: [PyMOL] algorithm for alignment >> >> Hi all, >> >> Anyone know which algorithm PyMOL uses to align or super of >> two structures? >> >> Thanks a lot! >> >> Best, >> Linda >> >> >> >> -------------------------------------------------------------- >> ----------- >> This SF.net email is sponsored by: Microsoft Defy all >> challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > |
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From: Lu L. <ll...@cs...> - 2008-01-26 06:28:16
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Hi Hally, Thank you for your reply! Could you tell me how to save the alignment result to a new .pdb file? Thanks again! Best, Linda Hally Shaffer wrote: > Linda, > > To align two proteins, they have to have the same number of atoms. You can > manipulate the pdb files to delete part of one protein or remove a small > molecule ligand if need be. You will need to save the "corrected" pdb files to > load for the alignment. > > Attached is a picture of two proteins I aligned (one is in the apo form and the > other is the ligand-bound holo form of the protein). The major difference > between the two is indicated in red. I had to load my two pdb files and then the > ligand (rea) as a separate pdb file. The commands are below. > > load 1LBDm.pdb, 1LBD > load 1FBYm.pdb, 1FBY > load REA.pdb, rea > > align 1LBD, 1FBY > > > Good luck, > Hally > -- > Hally Shaffer > <>< Graduate Student > Georgia Institute of Technology > School of Chemistry and Biochemistry > gt...@ma... > > > Quoting Lu Lin <ll...@cs...>: > > >> Hi all, >> >> Anyone know which algorithm PyMOL uses to align or super of two structures? >> >> Thanks a lot! >> >> Best, >> Linda >> >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> ------------------------------------------------------------------------ >> |
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From: Abhinav V. <abh...@gm...> - 2008-01-26 06:33:01
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there is something on the menu, file->save->molecule after the alignment, choose the molecule you want to save and just save. pymol saves the pdb with new coordinates. cheers, Abhi On Jan 25, 2008 10:29 PM, Lu Lin <ll...@cs...> wrote: > Hi Hally, > Thank you for your reply! Could you tell me how to save the alignment > result to a new .pdb file? > Thanks again! > > Best, > Linda > > Hally Shaffer wrote: > > Linda, > > > > To align two proteins, they have to have the same number of atoms. You > can > > manipulate the pdb files to delete part of one protein or remove a small > > molecule ligand if need be. You will need to save the "corrected" pdb > files to > > load for the alignment. > > > > Attached is a picture of two proteins I aligned (one is in the apo form > and the > > other is the ligand-bound holo form of the protein). The major > difference > > between the two is indicated in red. I had to load my two pdb files and > then the > > ligand (rea) as a separate pdb file. The commands are below. > > > > load 1LBDm.pdb, 1LBD > > load 1FBYm.pdb, 1FBY > > load REA.pdb, rea > > > > align 1LBD, 1FBY > > > > > > Good luck, > > Hally > > -- > > Hally Shaffer > > <>< Graduate Student > > Georgia Institute of Technology > > School of Chemistry and Biochemistry > > gt...@ma... > > > > > > Quoting Lu Lin <ll...@cs...>: > > > > > >> Hi all, > >> > >> Anyone know which algorithm PyMOL uses to align or super of two > structures? > >> > >> Thanks a lot! > >> > >> Best, > >> Linda > >> > >> > >> > >> > ------------------------------------------------------------------------- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyM...@li... > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > ------------------------------------------------------------------------ > >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
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From: Lu L. <ll...@cs...> - 2008-01-26 06:57:37
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Hi, Abhi, You mean save them separately? Is there some way to save them into one file? Thanks!! Best, Linda Abhinav Verma wrote: > there is something on the menu, file->save->molecule > after the alignment, choose the molecule you want to save and just > save. pymol saves the pdb with new coordinates. > > cheers, > Abhi > > On Jan 25, 2008 10:29 PM, Lu Lin <ll...@cs... > <mailto:ll...@cs...>> wrote: > > Hi Hally, > Thank you for your reply! Could you tell me how to save the alignment > result to a new .pdb file? > Thanks again! > > Best, > Linda > > Hally Shaffer wrote: > > Linda, > > > > To align two proteins, they have to have the same number of > atoms. You can > > manipulate the pdb files to delete part of one protein or remove > a small > > molecule ligand if need be. You will need to save the > "corrected" pdb files to > > load for the alignment. > > > > Attached is a picture of two proteins I aligned (one is in the > apo form and the > > other is the ligand-bound holo form of the protein). The major > difference > > between the two is indicated in red. I had to load my two pdb > files and then the > > ligand (rea) as a separate pdb file. The commands are below. > > > > load 1LBDm.pdb, 1LBD > > load 1FBYm.pdb, 1FBY > > load REA.pdb, rea > > > > align 1LBD, 1FBY > > > > > > Good luck, > > Hally > > -- > > Hally Shaffer > > <>< Graduate Student > > Georgia Institute of Technology > > School of Chemistry and Biochemistry > > gt...@ma... <mailto:gt...@ma...> > > > > > > Quoting Lu Lin <ll...@cs... <mailto:ll...@cs...>>: > > > > > >> Hi all, > >> > >> Anyone know which algorithm PyMOL uses to align or super of two > structures? > >> > >> Thanks a lot! > >> > >> Best, > >> Linda > >> > >> > >> > >> > ------------------------------------------------------------------------- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyM...@li... > <mailto:PyM...@li...> > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > ------------------------------------------------------------------------ > >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > <mailto:PyM...@li...> > https://lists.sourceforge.net/lists/listinfo/pymol-users > > |
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From: Martin <mar...@gm...> - 2008-01-26 10:11:58
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Am Samstag, 26. Januar 2008 schrieb Lu Lin: > Hi, Abhi, > You mean save them separately? Is there some way to save them into one > file? Thanks!! By default, the save command should save all (visible?) atoms. Should be in documentation of save. Any way you can also make a selection of your two molecules and save the selection to one file. Even if you have two files, "cat" will produce a single file quicker than loading them into pymol ;-) Best Martin |
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From: Tsjerk W. <ts...@gm...> - 2008-01-26 11:30:44
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Hi, 'save' will save all atoms by default, not only the visible ones. cat in Linux will surely be more efficient than loading in Pymol and saving, but the question related to alignment. cat doesn't do that for you. So the procedure would be: load A.pdb,A load B.pdb,B align A,B save AB-aligned.pdb Just one addition, Pymol may reorder the atoms. If this is okay (it won't matter for subsequent displaying), don't bother. Otherwise, before saving you might want to 'set retain_order,on' Cheers, Tsjerk On Jan 26, 2008 11:11 AM, Martin H=F6fling <mar...@gm...> wrote: > Am Samstag, 26. Januar 2008 schrieb Lu Lin: > > Hi, Abhi, > > You mean save them separately? Is there some way to save them into one > > file? Thanks!! > > By default, the save command should save all (visible?) atoms. Should be = in > documentation of save. Any way you can also make a selection of your two > molecules and save the selection to one file. > > Even if you have two files, "cat" will produce a single file quicker than > loading them into pymol ;-) > > Best > Martin > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > --=20 Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
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