Recommend deposition of input files

doc/mainpage.md

@@ -203,11 +203,16 @@ identifiers, but it can also detect other inputs, such as the templates used
 for comparative modeling. Thus, it is important for deposition that all input
 files are annotated as well as possible:
 
+ - deposit input files in a domain-specific database where possible and use
+   the deposited file (which typically will contain identifying headers) in the
+   modeling repository.
  - for PDB crystal structures, do not remove the original headers, such as
    the `HEADER` and `TITLE` lines.
  - for MODELLER comparative models, leave in the `REMARK` records and make sure
    that any files mentioned in `REMARK   6 ALIGNMENT:` or
-   `REMARK   6 SCRIPT:` records are available (modify the paths if necessary).
+   `REMARK   6 SCRIPT:` records are available (modify the paths if necessary,
+   for example if you moved the PDB file into a different directory from the
+   modeling script and alignment).
  - for manually generated PDB files, such as those extracted from a published
    work or generated by docking or other means, add suitable `EXPDTA` and
    `TITLE` records to the files for ProtocolOutput to pick up. See the