Merge branch 'develop' into dark-matter-metagenomics

projects/phytoplasma-effectors/README.md

+# Modelling of phytoplasma effectors
+
+[Link to project in ModelArchive](https://modelarchive.org/doi/10.5452/ma-saps) (incl. background on project itself)
+
+Setup:
+- Using AlphaFold v2.2 for monomer predictions with fairly default settings
+- Conversion based only on PDB files without extra data
+- CSV file with links to accession codes in UniProt
+
+Special features here:
+- Generic code added to find best sequence match in UniProt history and report mismatches
+- Sequences with remaining mismatches (here due to experimental assays) labelled in entity name
+- One obsolete entry (SAP11_MBS linked to A0A1B3JKP4 in UniProt or UPI00083DE1DE in UniParc)
+- pLDDT extracted from b-factors (simplest setup since no other QA scores anyway)
+
+Content:
+- translate2modelcif.py : script to do conversion
+- input_data: PDB files and CSV used for conversion

projects/phytoplasma-effectors/input_data/accessions.csv

+Accession,Name
+Q2NJQ2,SAP54 
+A0A0P7KHL3,SAP54_Peanut 
+A0A4Y5N0H8,SAP54_RP
+Q2NJD7,SAP49 
+Q2NJN9,SAP41 
+Q2NJB0,SAP66
+A0A410HXL4,SAP11_WBDL
+Q2NK94,SAP05 
+Q2NJA6,SAP11 
+Q2NII6,SAP13 
+Q2NKA4,SAP21
+Q2NJZ9,SAP27 
+Q2NIN8,SAP35 
+Q2NJL8,SAP42 
+Q2NJI2,SAP45
+Q2NJA8,SAP67 
+Q2NJA7,SAP68 
+Q2NK93,SAP06
+Q2NJJ6,SAP44
+Q2NJD6,SAP48
+A0A1B3JKP4,SAP11_MBS