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
python
# 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")
Cheers,
-- Jason
On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin
<jacob.pes...@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
>
> jacob
>
> <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>
> <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>
>
>
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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