Hi Simon

As far as know, Jmo reads the fisrt N lines of every file in search 
for tokens that will tell what format the file is in.

Your insertion of lines is probably making ti not reach the relevant, 
information-richs lines.

There was a similar problem recently reported with PDB files from a 
certain source that was inserting extra lines at the beginning.

You can force Jmol using a prefix like
load pdb::whateverFileName.ext
I'm not sure about the mmcif prefix, may it's that

See http://chemapps.stolaf.edu/jmol/docs/#load




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