#Chimera software mac os
#Chimera software full
#Chimera software code

Below, we describe the tools in more detail and discuss their advantages and disadvantages relative to other programs. These tools work together within Chimera to enhance the understanding of sequence information in the context of structure and vice versa. Completing the cycle, the Match -> Align extension constructs sequence alignments from pre-existing superpositions of structures. A novel score incorporating both secondary structure and residue type is used to align the sequences. If one does not already have a sequence alignment, the MatchMaker extension can be used to generate sequence alignments and superimpose structures accordingly. Structures can be superimposed using the alignment, and sequence-related data such as conservation can be shown on the structures. The Multalign Viewer extension of Chimera displays sequence alignments and automatically associates structures with sequences in the alignment.

A suite of tools within UCSF Chimera has been developed for studying sequence-structure relationships and comparing related structures.Ĭommon tasks in sequence-structure work include: (A) displaying information from a sequence alignment on one or more corresponding structures, or displaying information from the structures on the alignment (B) superimposing structures so that they can be compared (C) generating a structure-based sequence alignment. Integration of protein sequence and structure information is essential in many problem domains, including structural biology, protein engineering, and drug design.

#Chimera software mac os

UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines.

The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences.

#Chimera software code

Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.

Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures.

We describe enhancements to UCSF Chimera to achieve these goals.

#Chimera software full

and (d) interoperate with each other and with a full complement of molecular graphics features. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit) (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc. Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research.