Morphs: Difference between revisions
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The [http://molmovdb.org Yale Morph Server] from Mark Gerstein's group. In addition to the chemically possible nature of the results, this server is very attractive because it totally automates both the creation of the multiple-model morph PDB data file, and also its visualization. The server does the structural alignment of the starting PDB files, and can handle modest differences in sequence between the initial and final PDB files. It then does a linear interpolation followed by some energy minimization to render each frame ''chemically possible''. | The [http://molmovdb.org Yale Morph Server] from Mark Gerstein's group. In addition to the chemically possible nature of the results, this server is very attractive because it totally automates both the creation of the multiple-model morph PDB data file, and also its visualization. The server does the structural alignment of the starting PDB files, and can handle modest differences in sequence between the initial and final PDB files. It then does a linear interpolation followed by some energy minimization to render each frame ''chemically possible''. | ||
One disadvantage of the Yale Morph Server is that you cannot control the alignment of the starting and ending structures. | |||
====Proteopedia PyMOL Morpher==== | |||
For straightforward morphs, Proteopedia provides a page http://proteopedia.org/cgi-bin/morph that sends a morph request to the [https://pymol.org/2/ PyMOL program] and automatically uploads the resulting multi-model file to proteopedia. An example of a morph made by the server is [http://proteopedia.org/wiki/index.php/Image:Morph_semet_apo-chaind.pdb_zn_complex-chaina.pdb_u4043.pdb here], and it is shown on this [http://proteopedia.org/wiki/index.php/User:Kristian_Koski/P4H#flexible_loops page]. | For straightforward morphs, Proteopedia provides a page http://proteopedia.org/cgi-bin/morph that sends a morph request to the [https://pymol.org/2/ PyMOL program] and automatically uploads the resulting multi-model file to proteopedia. An example of a morph made by the server is [http://proteopedia.org/wiki/index.php/Image:Morph_semet_apo-chaind.pdb_zn_complex-chaina.pdb_u4043.pdb here], and it is shown on this [http://proteopedia.org/wiki/index.php/User:Kristian_Koski/P4H#flexible_loops page]. | ||
====FATCAT, Burnham Institute==== | |||
The [http://fatcat.burnham.org FATCAT Structural Alignment Server] also produces "chemically possible" morphs. After an optionally flexible alignment (permitting twists at hinge points determined by FATCAT), a linear interpolation is done between the aligned models. Then "the intermediate structures are optimized by energy gradient minimization employing a reduced representation force field." | The [http://fatcat.burnham.org FATCAT Structural Alignment Server] also produces "chemically possible" morphs. After an optionally flexible alignment (permitting twists at hinge points determined by FATCAT), a linear interpolation is done between the aligned models. Then "the intermediate structures are optimized by energy gradient minimization employing a reduced representation force field." | ||
====Biomolecular Morphing by Kleywegt at Uppsala==== | |||
Another way to make "chemically reasonable" morphs is available from the [http://xray.bmc.uu.se/usf/mol_morph.html Biomolecular Morphing] site by Gerard J. Kleywegt at Uppsala University, Sweden. Unlike the Yale server, this is not a server where you can submit a job and get back finished results automatically. Kleywegt's LSQMAN software is downloadable for use on linux, and is free for academic and non-profit use. | Another way to make "chemically reasonable" morphs is available from the [http://xray.bmc.uu.se/usf/mol_morph.html Biomolecular Morphing] site by Gerard J. Kleywegt at Uppsala University, Sweden. Unlike the Yale server, this is not a server where you can submit a job and get back finished results automatically. Kleywegt's LSQMAN software is downloadable for use on linux, and is free for academic and non-profit use. | ||
