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Auto molecular replacement

Auto molecular replacement. Automatic molecular replacement. Basic philosophy: Users are very clever but they do not have sufficient time to try all parameters Procedures must use only existing data (reflection file, sequence/name of protein) and make decision using them.

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Auto molecular replacement

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  1. Auto molecular replacement

  2. Automatic molecular replacement Basic philosophy: Users are very clever but they do not have sufficient time to try all parameters Procedures must use only existing data (reflection file, sequence/name of protein) and make decision using them. Use of existing software with minimal modification Existing programs/software can be developed further and procedure will gain from it without readjustment. They may have been written a long time ago. They can be third party software. Use available information from PDB as well as experience Organise PDB in a usable form, add protocols that worked for various users.

  3. SF and sequence or PDB DB Data Base SFCHECK Manager It can make complicated decisions. It is in OO and programs or procedures are classes. Subunit and domain structure of all proteins MOLREP Hierarchical organisation according to homology REFMAC Others X-ray programs and protocols. These are examples Solved structure or not

  4. Organisation of “DB” • pdb files classified by homology • Domain structure of each protein • Dimer and high level of organisation of each molecule • (perhaps later) Fragments of various lengths • (later) Intensity curves for various types of macromolecules • etc This part can in principle organised using entity relational DB technology.

  5. Manager Written in python. It already has: classes (or wrappers) for SFCHECK, MOLREP and DB_SEARCH. All programs are replaceable. needs to have: REFMAC and others Communications are using xml. Manager knows what it needs and then particular program is modified to add necessary info in a form that can be processed. This part needs to be written using OO technology

  6. Others It does not matter if you can write python (or else) “classes” around it. Language is secondary, algorithm is primary. E.g. I would not write another SHELXD but would use it if I can get hold of license so that G.S. gets credits (and money if there is any). This part can be written in any language as soon as it obeys certain conditions. Components must work sufficiently well and fast. Detailed algorithms are here.

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