Update README.md

README.md

@@ -43,9 +43,9 @@ turterra
         |--smiles.tsv
         |--structure_alignment.fasta
         |--structures
-            |--sequence1_model.pdb
-            |--sequence2.pdb
-            |--sequence3_model.pdb
+            |--accession1_model.pdb
+            |--accession2.pdb
+            |--accession3_model.pdb
             |--...
         |--tree.txt
 ```
@@ -56,6 +56,9 @@ turterra
 | sequences.fasta | A .fasta file containing all the sequences in the analysis, with the accessions specified in data.txt as headers. |
 | sequence_alignment.fasta | A .fasta file containing an alignment of all sequences in the analysis, with the accessions specified in data.txt as headers. |
 | smiles.tsv | A tab-separated file, with as header 'Name\tSMILES', and all compounds names in the analysis and their corresponding structures in [SMILES format](http://opensmiles.org/opensmiles.html). |
+| structure_alignment.fasta | A .fasta file containing a structure-based sequence alignment of all sequences in the analysis, with the accessions specified in data.txt as headers. We recommend you create this file with [caretta](https://github.com/TurtleTools/caretta) through turterra-build. |
+| structures | Directory containing structural (homology) models for sequences in the analysis in .pdb format. File names should have the format 'accession_model.pdb' for homology-modelled structures, and 'accession.pdb' for crystal structures. Accessions should match the accessions in data.txt. |
+| tree.txt | A phylogenetic tree in newick format. Leaf nodes should be labelled with the accessions specified in data.txt. |