Differences

This shows you the differences between two versions of the page.

--- prepare_files [2016/05/25 13:23] – created bonnefon
+++ prepare_files [2023/11/01 20:18] (current) – external edit 127.0.0.1
@@ Line 2: / Line 2: @@
 The final PDB file and the cleaned MTZ file are required.
+In the PDB files the first lines should be deleted, up to the line written
+<code>REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP.</code>
+Only polymer chains should finish with a <q>TER</q>, remove all other <q>TER</q> present for the ligands or water molecules.
+Coordinates may be deposited as either mmCIF or PDB formatted files. We encourage you to use pdb_extract to prepare mmCIF formatted file. If you are using a PDB formatted coordinate file, please check the following PDB format requirements prior to file upload:
+  * A TER record is placed at the end of every polymeric chain.
+  * TER records are not present within a polymeric chain. Some refinement packages insert extra TER records at gaps within a chain. Please remove the extra TER records.
+  * No TER records should be included at the end of non-polymer residues such as ions, ligands, or waters.
+  * PDB format files with misplaced TER records will result in incorrect format translation and data extraction – which may result in data loss during annotation.
+  * Depositions comprised of multiple models should include MODEL and ENDMDL records. The models should be listed sequentially in columns 11-14.
+  * If there are alternate conformations in the structure, the alternate conformation indicator must be provided in column 17 of ATOM and HETATM records.
+  * There should be only one END record at the end of the file.