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Xray

Protein X-Ray Model Building

The following two files for the 46-residue plant-seed protein crambin, derived from the x-ray structure (Brookhaven code 1crn), can be found in Moloc's data directory moloc/dat: crbn.pdb (structure), crbn.mpf (calculated electron density map). In order to save disk space the map resolution is rather low.

Prepare Incomplete Structure

Rebuild Deleted Loop

The Calf structure is now complete, but the conformation may not optimally fit into the electron density (although we have arranged for a reasonable position of the new residues). There are a couple of tools in Moloc to modify peptide conformations. They can be found in the 'forge' and 'Calf building' menus, but have been collected in a separate menu 'xry/m' (modifying (forging) Calf structure) in order to have the frequently used options ready at hand.

Modify C-alpha Structure

In Moloc, protein structures can be modified interactively at the C-alpha level. By this token, the view is kept simple, while all degrees of freedom can still be varied.

Search Database for loop conformations

The residues of the loop must already be present in the structure, albeit in an arbitrary conformation.

Real Space Refinement of Newly Built Stretch

Moloc offers the possibility to adjust conformations automatically by running a force field minimization in which the electron density provides an additional force term.

Structure Update after Building

Structure building in Moloc makes use of its reduced C-alpha representation. However, at the end, or for refinment a full (all atom) structure is needed. From the C-alpha structure coordinates of non-C-alpha atoms are reconstructed by algorithm. Even if the C-alpha structure remained unchanged, the result may slightly deviate from the start structure. In order to keep the original coordinates for unchanged residues, Moloc provides update procedures for various cases: Do not hesitate to save your work from time to time. No program is totally crash-save!

Further X-ray Tools

Further available options are only listed here without detailed demonstration:

Modify a Ligand

A ligand is modified by the standard building tools in Moloc. However, when the structure originates from a .pdb File it is specified as monomer of a polymer and carries corresponding information which may interfere with the building process. How to deal with this is subject of a separate topic.

Data Generation for Third-Party Software

While force-field parameters or geometric reference values are commonly available in other programs for proteins, nucleic acids, and a few common biomolecules, it is not always straightforward to obtain such values for general organic molecules as usually encountered e.g. in medicinal chemistry. Since Moloc's force-field MAB is based on a generic parametrization it is able to provide parameters for these cases. In order to facilitate the combined use of third-party software, files containing the necessary data for running the following programs can be generated: To generate such files, choose option 'dyn/g' (generate geometry-, topology-, and parameter files).