Subject: Re: [nmr_sparky] water refinement of structures generated by CYANA
From: Betty Swanson
Date: Nov 4 5:49 PM

Previous: 447

Thanks you all for so many suggestions.
Betty

Matthew Revington mrevingt2@... wrote:
My recollection is that you have to set up a directory
like the one in the example provided with your cyana
restraints converted to cns .tbl files , a .mtf file,
your 20 best cyana files in the str/wt directory. I
found then that the script that controls the actual
calculation is the re_h2o.sh script and it has to be
run in the directroy above the one containing the .tbl
and .mtf files, it needs to edited for paths and
other specific paths and it is erased at the end of
the run so it is a good idea to make a copy before
trying it.

When paths are all set right and your scripts are not
found it is very often a shell problem, ie are you
running in csh or sh or etc

--- Mandar T. Naik mandarn@ibms. sinica.edu. tw
wrote:

Hi,
Another alternative is discussed in message 222 of
CYANA mailing list by Jin-Won Jung. Their python
scripts are available at

http://spin. yonsei.ac. kr/solwind/ h2orefine. tar.gz.

regards
-mandar

On Sunday 28 October 2007 10:56, Betty Swanson
wrote:
Dear All,

I want to carry out water refinement of CYANA
generated structures using CNS1.1. Can you’ll please
help me out? I know there are RECOORD scripts such
as generate.sh etc. However, I don’t know how to
execute them. For instance, simply typing

“generate.sh 1KDF.pdb”

does not generate any output. It just gives the
following message:

generate.sh: command not found.

(I have changed the path such that the location
of the RECOORD scripts are defined).

Since some of you’ll must have done
waterrefinement of structures generated by CYANA,
can you please tell me how to do it.

Thanks,

Betty




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