Morph Server
From Info
Notes: The molecular viewer currently being used by MolMovDB is Jmol, which may raise compatibility issues with Chrome and Firefox. We are currently upgrading the viewer to use JSmol, which will be more compatible with standard browsers. Also, for the time being, we are not archiving morphs for long-term storage. Please retrieve your morph result(s) within a few days of job submission. We apologize for any inconvenience this may cause.
Please submit your structures at one of the three forms of the server listed below:
3. Morph2 Server A variation of Morph Server for morphing between conformations of different but related proteins.
4. Older version of multi-chain morph server for morphing nucleic acids.
The server will produce 2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations. The single chain server handles mutations, missing atoms and residues, and even homologous structures. The multi chain server allows morphing of large complexes, with mutations and/or deletions. You may provide either a pair of PDB identifiers, or structures uploaded from your web browser, or a combination of the two to morph. This process may take anywhere from five minutes to half an hour to complete, depending on the size of the structures and the load on the server. You will receive notification by email when your morph is complete.
Current constraints include:
- The original server requires the SEQRES header for optimal interpretation of the PDB files. However, this may sometimes lead to severely truncated or gapped structures. Only a single chain can be morphed. Ideally, structures should have close to the same number of amino acids. (It is, however, possible to obtain very high-quality movies of pairs of structures with as little as 50% sequence identity, in cases where the structure is well-conserved.)
- The multi-chain server will determine sequence directly from the ATOM records; this seems to work well so far. Original residue numbering will be maintained if possible. Mismatched residues will be mutated to alanine.
- The older multichain server requires exactly matching residues in the input files.
- Some non-standard/modified residues may not be processed correctly; in the multi-chain server, we have tried to accomodate these by converting them to the closest "normal" residue, e.g. selenomet to methionine, phosphorylated residues to the unphosphorylated version. This may not always work (if you notice, please let us know!).
All versions of the server use energy minimization to calculate the intermediate frames, which produces results that are usually much better than morphs made by simple linear interpolation, but still runs relatively quickly on modern hardware. A new method of interpolation using the program FRODA (Thorpe lab, ASU) is also available, and may be successful where the original fails to generate a reasonable interpolation.
In addition to being more flexible, the original server calculates a large number of statistics and performs sieve-fitting on the structures. All morphs are entered into the database for future analysis. You are welcome to download and use all output files and movies for your morph as long as you follow the citation guidelines.
In addition to being more flexible, the original server calculates a large number of statistics and performs sieve-fitting on the structures. All morphs are entered into the database for future analysis. You are welcome to download and use all output files and movies for your morph as long as you follow the citation guidelines.
Further information is available from a more detailed description of the server or the frequently asked questions list, as well as the original paper. You may also contact us by mailing "motions@bioinfo.mbb.yale.edu".
A number of third-party programs are essential to the server, including X-PLOR, CNS, PyMOL, AMPS, MolScript, and SAMPEG. You may obtain certain portions of the server (including a standalone CNS script for morphing) by arrangement with the authors.
