Morphs: Difference between revisions
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''Chemically possible'' (also sometimes called ''chemically plausible'', ''semi-plausible'', or ''chemically reasonable'') means that, at the least, correct covalent bond lengths and angles are maintained, and that atoms are constrained not to pass through each other. This type of morph requires sophisticated software, but luckily that is freely available and easy to use at 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''. | ''Chemically possible'' (also sometimes called ''chemically plausible'', ''semi-plausible'', or ''chemically reasonable'') means that, at the least, correct covalent bond lengths and angles are maintained, and that atoms are constrained not to pass through each other. This type of morph requires sophisticated software, but luckily that is freely available and easy to use at 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''. | ||
For straightforward morphs, Proteopedia provides a page http://proteopedia.org/cgi-bin/morph that sends a morph request to the 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]. | ||
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." | ||