Morphs: Difference between revisions

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====Yale Morph Server====

''SADLY, AS OF 2020, THE YALE MORPH SERVER AND GALLERY OF MOLECULAR MOVEMENTS HAS BEEN OFFLINE FOR A NUMBER OF YEARS.'' ~~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''.~~

''WORKING AGAIN in February, 2021. Their animation player doesn't work because it still requires Java, but you can download the morph PDB file and animate it in Proteopedia or Jmol.''

~~One disadvantage of the~~ Yale Morph Server is ~~that you cannot control~~ the alignment of the starting and ~~ending~~ structures.

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''.

Morph2 (version 2) of the Yale Morph Server allows you to pre-align (or have the server align) your structures, and gives you the option of minimizing, or not.

===Linear Interpolation===

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@@ Line 140: / Line 140: @@
 ====Yale Morph Server====
-''SADLY, AS OF 2020, THE YALE MORPH SERVER AND GALLERY OF MOLECULAR MOVEMENTS HAS BEEN OFFLINE FOR A NUMBER OF YEARS.'' 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''.
+<!--''SADLY, AS OF 2020, THE YALE MORPH SERVER AND GALLERY OF MOLECULAR MOVEMENTS HAS BEEN OFFLINE FOR A NUMBER OF YEARS.''-->
+''WORKING AGAIN in February, 2021. Their animation player doesn't work because it still requires Java, but you can download the morph PDB file and animate it in Proteopedia or Jmol.''
-One disadvantage of the Yale Morph Server is that you cannot control the alignment of the starting and ending structures.
+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''.
+Morph2 (version 2) of the Yale Morph Server allows you to pre-align (or have the server align) your structures, and gives you the option of minimizing, or not.
 ===Linear Interpolation===