Hello Vitaly--
>
> 1. Is there a way to write the energies in the PDB file at the
> intermediate stages? PDBTool.write() seems to produce the coordinate
> files only.
Are you looking to produce a trajectory of energies? If you want only
a small number of energies, you can add these to the REMARKS section
of the pdb file by using the addRemark() method. i.e.
energy = pot.calcEnergy()
from pdbTool import PDBTool
pdb=PDBTool("file.pdb")
pdb=PDBTool.addRemark("intermediate energy = %f" % energy)
.
.
.
pdb.write()
You can also add remark entries to the files printed with
writeStructure:
def calcOneStructure(loopInfo):
.
.
.
energy = pot.calcEnergy()
remarks = "intermediate energy = %f" % energy
.
.
.
loopInfo.writeStructure(extraRemarks=remarks)
return
>
> 2. Could you please clarify the "constraints interaction"
> (http://nmr.cit.nih.gov/xplor-nih/xplorMan/node135.html) construction?
> It seems that in each "constraints" statement every atom can be
> selected just once, e.g. the construction below will maintain the
> weights of 1, despite the second "interaction" statement.
> constraints
> interaction (segid A) (segid A)
> weights * 1 end
> interaction (segid A) (segid A)
> weights * 0 end
> end
each interaction statement creates a new set of interactions. So, the
second line has no effect on the energy value. If you specify a weight
of 1 instead of zero, the effect should be to multiply segid A
energies by 2. I hope...
> When do
> these constraints get reset?
They get reset at the next constraints statement.
> Is it possible to echo the current
> interactions and the weights?
Not to my knowledge.
I find this construct fragile and otherwise difficult to use, and try
to avoid it, if possible.
>
> Does this selection algebra also apply to the IVM objects in Python
> interface, e.g. which residues will remain fixed upon the following
> statement?
> dynamics.fix('segid A')
> dynamics.fix('segid A and resi 1:10')
>
constraints interaction in the old XPLOR interface is completely
separate from the python/C++ stuff. The above statements are
equivalent to
dynamics.fix('segid A and resi 1:10')
best regards--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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