Hi Jacob,

Use the result from cmd.cealign and an "alignment object". Here's an example:

# fetch two proteins

fetch 1cll 1ggz, async=0

# use a python block


# cealign the two structures and create a corresponding "alignment" object

result = cmd.cealign("1cll", "1ggz", object="aln")

# print out the values from the result

print result.keys()
for key in result:
  print "%s: %s" % (key, result[key])

# end the python block

python end

# now access those atoms in the alignment

select 1cll and aln

# or count the atoms in 1ggz and aln

print cmd.count_atoms("1ggz and aln")


-- Jason

On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin <Jacob.Pessin@einstein.yu.edu> wrote:
Hi all,

can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail).

thanks in advance


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Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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