Problem: Under Windows, the xxx_GetFile utilities do not keep the file extensions of the imported files in the worksheet name and therefore do not recognize the individual worksheets properly. For the moment, these macros will only work correctly if you remove the .rsa filename extensions from the filenames. I will correct the problem as soon as possible.

Macros:

AA_CDR_Arrange counts number of valid amino acid within the selected rows, consolidates gaps and places them in the center of the sequence block, centering the consolidated gaps on a given sequence position.

AA_Charge colors the selected amino acids according to charge: acidic residues (Asp, Glu) are colored red, basic ones cyan (His) and blue (Lys,Arg)

AA_Composition determines the amino acid composition of all sequences in an alignment

AA_Convert_3to1 converts a sequence alignment from 3-letter code to 1-letter-code (for KABAT database), replaces the input triplett by the output letter => duplicate the worksheet before translating. Cells containing uninterpretable data or comment indicators are highlighted.

AA_Convert_NtoAA translates nucleotide code to 1-letter amino acid code. Replaces nucleotides with amino acids => duplicate the worksheet before translating. Requires worksheet "code" in AHo_macros.xls. Each cell has to contain one nucleotide triplet.

AA_Cys highlights Cys residues in a sequence alignment. The macro can easely by changed to highlight any other amino acids

AA_DefineColors defines the color map of an EXCEL workbook or worksheet to ensure that the alignment is colored as intended, independent of the version of EXCEL used. Run this macro before applying any of the coloring macros.

AA_Delete_Identical

AA_Differences Colors a sequence alignment in such a way that the differences between neighboring sequences are highlighted and counts the number of differences between a sequence and the next one in the alignment

AA_Empty Fills empty cells with the gap character "." and colors them black.

AA_Freq

AA_FreqDistribute rearranges a series of tables generated by AA_Frequency in such a way that the results for each residue position are collected in a separate table on a separate worksheet

AA_FreqFormat

AA_Frequency determines the frequency of different amino acids in each position of a sequence alignment, the consensus sequence, the percentage of sequences which agree with the consensus and the Kabat sequence variability at this position.

AA_FreqValColor colors the table generated by AA_Frequency by value

AA_Hydropathy colors cells according to amino acid hydropathy (Parameters of Kyte+Doolittle, J. Mol. Biol. 157(1982)105-132)

AA_Parse converts a text string in a single cell into individual characters in consecutive cells. You can select a range of cells within the same column. Do not select more than one column, cells to the right of this column will be overwritten by the parsed sequence. To parse sequences with more than 250 AA per line you have to cut them into smaller pieces during the fixed-format inport or by using the substring-function and process the pieces separatly

AA_Parse_3Letter converts a text string into tripletts of characters in consecutive cells, assuming one separation character, converting e.g. Amino acid sequences in 3-letter-code or nucleotide tripletts. You can select a range of cells within the same column. Do not select more than one column, cells to the right of this column will be overwritten with the parsed sequence.

AA_SeqLength counts number of valid amino acid within the selected sequences. The result is placed in the column following the selected sequence block.

AA_SeqVarColor converts the Kabat sequence variability values to a color code

AA_Similarity colors a sequence alignment according to similarity to a reference sequence. Calculated %sequence similarity, % sequence identity and the length of each sequence

AA_Type colors a sequence alignment by amino acid type: Tyr, Phe, Trp: orange; Leu, Ile, Val, Pro, Ala, Met, Cys: yellow; Gly: green-yellow; Thr, Ser, Asn, Gln: green; His: cyan; Arg, Lys: blue; Asp, Glu: red

PDB_CollectData collects the sequence information, residue labels and chain identifiers of all structures into three worksheets called "SEQ", "LABEL" and "CHAIN"

PDB_DeleteWater deletes water records (ATOM or HETATM recods with residue labels "WAT", "HOH" or "H2O")

PDB_ExtractSeq Converts the vertical sequence alignment (in three-letter code) in worksheet "SEQ" into a horizontal one in worksheet "ALIG"

PDB_GapFromAlig: Propagates the gapping and labelling information from the alignment to worksheets "SEQ", "LABEL" and "CHAIN"

PDB_GapFromLbl gaps worksheets "SEQ", "LABEL" and "CHAIN" as specified by the residue label. This gapping is retained as the sequence alignment is extracted by PDB_ExtractSeq.

PDB_GapfromSeq has to be used for sequences longer than 250 residues. In this case, the manual gapping is applied to the "SEQ" worksheet and propagated to the other two worksheets by this macro.

PDB_GetFiles reads the PDB coordinate files whose filenames are listed in the first column of the worksheet "Files" into separate worksheets of the active workbook

PDB_PutFiles exports the relabelled PDB Files as individual ASCII text files

PDB_reLbl relabels the residues according to the information contained in the "SEQ", "LABEL" and "CHAIN" worksheets

RSA_CollectData collects the sequences, residue labels and accessibility data from multiple .rsa worksheets into individual worksheets

RSA_ColorAlig

RSA_ColorVal

RSA_ExtractSeq extracts the sequences from the "SEQ" worksheet to a horizontal alignment (works only for sequences with less than 250 residues)

RSA_GapFromAlig propagates alignment information from the horizontal alignment to the worksheets collected by "RSA_CollectData"

RSA_GapFromLbl gaps the worksheets collected by "RSA_CollectData" according to the residue label

RSA_GAPFromSeq gaps the worksheets collected by "RSA_CollectData" according to the gaps placed in the "SEQ" worksheet

RSA_GetFiles reads the .rsa residue surface accessibility files whose filenames are listed in the first column of the worksheet "Files" into separate worksheets of the active workbook

RSA_ValColorBlue converts relative accessibility values to a color code

RSA_ValColorRed converts relative solvent accessibilitiy differences to a color code

RSA_ValDiff

STR_CaDist

STR_CollectData

STR_ColorAlig

STR_ColorVal

STR_ExtractSeq

STR_GapFromAlig

STR_GapFromLbl

STR_GapFromSeq

STR_GetFiles

Tab_HideZero()

File Formats

ASA-Format: Format of the atom accessibility file generated by the program NACCESS. basically corresponds to a PDB file with the solvent accessibility of the atom in the field normally used for the temperature factors

PDB-Format: Format description of the PDB ATOM and HETATM records

RSA-Format: Format of the residue accessibility file generated by the program NACCESS