I get a segmentation fault when run on 1AT1 and 1RAA with blockfator 2.  This is not the case when I compile with -finit-local-zero option.  Perhaps I should always use this. 


In pointdist.f "10 CONTINUE" was deleted as was unused.
In extstop2.f put NOCONDOM to zero at beginning (uncommented already there)
In cluster2_1.f "123 CONTINUE" was deleted as was unused.

Outputs TER at end of all chains.  Before if the two chains had the same chain id this did not happen.  Two chains can be the same if they are from different models which is the case for PDB biologial units.  In 3ddyndom the model number ismonitored in order to achieve this.
 
Now output files "_pdb" and "_rotvecs" now become "structure.pdb" and "rotvecs_pdb" respectively.  "_info" becomes "_info.txt".  This makes things easier on windows.  These changes were made in inoutputR.f 

I have removed the "IF (AC.EQ....) in readpdb.f for eliminating alternative conformations.  This is not needed now as Chris's program already does this.

In the original DynDom the maximum residue number is from the last atom in the final chain.  However, in DynDom3D for the server this is no good as the number of the final residue in the final chain may be less than the largest residue number in some other chain. This can cause the arrow colouring to wrongly colouring some residues in the molecule. In order to remedy this the maximum residue number RESMAX is determined in readpdb and passed on to arrow.

Atoms are numbered from 0 as requested by Chris as this is how Jmol does it.

DynDom3Dv1.04

Removed statement "WRITE(6,*)' NO RESULTS. TRY CHANGING YOUR PARAMETERS '
in cluster2_1.f and in 3ddyndom.f put this statement after exiting cluster routine with nullres=.true. so that this statement appears for all null results.
