-
Copy molecule /MOL to /BACKUP, e.g. to make a backup copy of the original
conformation before doing something drastic, e.g. energy minimization using
the Tripos Force Field ("save early , save often"):
-
Copy molecule /SPH1000016 to /protX/L/LIG_1, e.g. to form a protein / ligand
complex between /protX (hierarchical protein / chain / residue /atoms structure)
and the ligand /SPH1000016 ("flat" molecule /atoms structure):
copy /SPH*16 /protX/L/LIG_1
Note: wild-cards may be used in source and target
specifications, provided that the source and/or target is
uniquely determined by the wild-card string.
-
After inserting a new residue, LEU_281A. into a protein chain, /4apr/E,
we want to put the new residue into its proper sequence, following residue
PHE_281 (some inferior modeling programs put all insertions at the end
of the structure file, irrespective of the natural sequence given by connectivity):
move -mol /4apr/E/LEU_281A -after /4apr/E/PHE_281 LEU_281A
Note: it is not necessary to give the full name of the target,
since the prefix (/4apr/E) can be inferred from the full name of the insertion
point (/4apr/E/PHE_281). The same operation, using old syntax, would be:
move /4apr/E/LEU_281A /4apr/E/ after PHE_281
Note: here we have not specified a name for the target residue
( target ends with a slash "/"), and so the old name (LEU_281A)
is used by default. Also, the short name for the insertion point (PHE_281)
could be used, since the full name can be inferred from the full name of
the target, and from the fact that an "after" insertion point must have
the same parent prefix as the target.
-
The asymmetric unit the file 4apr.pdb from the Brookhaven Database (/4apr/A)
contains two chains (enzyme /4apr/A/E and inhibitor /4apr/A/I) and 312
water molecules (/4apr/A/HOH_501-HOH_885) which are not in a named chain.
The following move command converts this non uniform structure (water
atoms at level four, protein and inhibitor atoms at level five) into a
uniform structure (all atoms at level 5):
move -atoms /4apr/A/HOH_* -done /4apr/A/W
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What if the insertion in Example C would have been a whole loop, rather
than a single residue? Assume we have inserted a four residue loop (LEU_281A
to HIS_281D), and that we would like to move the loop into its proper sequence.
This could be achieved by moving the four residues individually, as in
Example C. A slightly quicker 2-step procedure is to
move -atoms /4apr/E/*_281A-*_281D-done /ext
merge /4apr/e -after *_281 /ext
Note: The atomselection in the move command has chain
/4apr/E as common root. The selected atoms are extracted into /ext, preserving
the residue structure from /4apr/E down. The extracted structure is then
merged with chain /4apr/E, starting to insert residues of /ext after residue
*_281 of /4apr/E.