NCSymm:

Detection of Non-Crystallographic Symmetry

PART II: By Substructure

This program detects NCS from a set of substructure solutions. Each heavy atom location in Cartesian coordinates is called a site. This program results in a table of site IDs. All sites in a row are related by non-crystallographic symmetries. All sites in a column are from a rigid, nominal monomer. An NCS relationship from one monomer (column) to another is described by a rotation matrix and a translation vector. Those sites that do not agree with the recognized NCS are listed as erroneous sites, if any. Missing sites from the original substructure solutions will be completed.

To use this program online, simply fill the form after reading some brief comments below, and upload a substructure file in PDB format. Results will be returned shortly, if the calculation can be done on-the-fly, or otherwise will be sent back to you by E-mail later.

To obtain a license of this program, please contact Renz Research, Inc.


About You

Name:
Institution:
E-mail:

About Your Crystal

Cell

a: b: c:
alpha: beta: gamma:

Symmetry

Space group: Nasymm: monomers per asymmetric unit

Monomer Size

Patterson radius is a control parameter for the calculation. It can be automatically estimated if a rough value of monomer size is known in either physical dimension, or molecular weight, or number of residue. Patterson radius can also be specified directly.

Substructure

Error tolerance in Angstrom:
Noisy substructure:

The PDB file must contain Cartesian coordinates for heavy atom sites only, and must use keywords ATOM or HETATM. Each atom must have a unique ID number. A site with lower temperature factor has higher priority to be chosen as a reference, or top site has higher priority if temperature factor is a constant. All fields other than keyword, ID, coordinates, and temperature factor are ignored. Error tolerance and noisy flag may alter the program's performance.



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Copyright © 2003 John Zhong Ren
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