ColoringSequence StatisticsRenumberingAccessibilityTorsion AnglesStructural VariabilityHydrogen BondsDownloads

EXCEL Macros

We provide a series of Microsoft EXCEL VISUAL BASIC macros, which facilitate the import of sequence alignments and other, structure-related data such as coordinates, lists of solvent accessibility, torsion angles and hydrogen bonds, from ASCII text files generated by external programs (e.g. GCG "pretty" Files) into an EXCEL workbook and present them in a way more easily accessible to the human eye than large tables of numeric values. One way to achieve this is to color the sequences according to different coloring schemes.

The macros are not meant to be fully automated programs, but to provide a flexible set of tools for manipulating the type of data encountered in the comparative analysis of protein sequences and structures, which can easily be adapted to the individual needs of a particular user. Therefore we provide at this web site a detailed annotation of the source code, which makes it easier for a user who is not familiar with programming to adapt a macro to different input file formats or to new tasks. The macros have been tested on Microsoft EXCEL 98 for MacOS and Microsoft EXCEL 97 and 2000 for Win.

Proceed to "Download" for an EXCEL Workbook containing the entire macro collection

Download Macros

Caution: Do not rename the workbook "AHo_macros.xls", since some of the macros need to access parameter files contained within the workbook.

For documentation purposes, the macros have been grouped according to the tasks they perform:

The sequence import macros facilitate the import of sequences and sequence alignments into EXCEL. They also contain utilities to convert from 3-letter code to the 1-letter code used by the other macros, to convert nucleic acid triplets to amino acids (rudimentary) and to post-process sequence alignments

The coloring macros color sequence alignments according to different properties of the amino acids: Amino acid type, hydrophobicity, similarity to a reference sequence, etc. Auxillary macros help to import sequence alignments from external sources into an EXCEL workbook and to define the EXCEL color map independent of the version of EXCEL you are working with. They work with data which can be derived directly from the sequences, using amino acid-specific parameters contained in the same workbook as the macros.

The sequence statistics macros extract the position-dependent amino acid distribution, consensus sequence and sequence variability from a given sequence alignment.

The renumbering macros are used to renumber a series of PDB coordinate files containing homologous structures according to a common numbering scheme. A common numbering scheme for the related structures greatly facilitates the further analysis of derived data.

The accessibility macros use the output of the program NACCESS to color sequence alignments according to the solvent accessibilities of the residues and to identify the contact residues of interfaces in a complex from the differences in residue solvent accessible surface in the complex and the isolated domains.

The torsion angle macros allow to collect multiple files containing lists of main-chain torsion angles generated by the program INSIGHT II (MSI/Biosym), collect the torsion angles of equivalent residues in multiple structures and plot them as ramachandran plots. Positions of positive phi angles are highlighted in the sequence alignment

The Ca variability macros allow to import sets of 3D-prealigned PDB coordinate files to calculate the average Ca-Positions and the deviation of individal structures from this average

The hydrogen bond macros allow to compare and analyze the hydrogen bonding pattern in multiple related structures based on imported lists of hydrogen bonds

Click here for an alphabetical list of all macros

AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Wednesday, March 19, 2008