[phenixbb] Any real space map-mask / NCS utility?

Tom Terwilliger terwilliger at lanl.gov
Thu May 22 08:08:17 PDT 2008

Hi Partha,

I think we don't have a tool for just what you want...but here is an 
idea given what you are trying:

In coot build a short piece of polypeptide in the region where one ha 
site is located.  Match the map in some way.  Now rotate/translate 
this exact piece of chain over to your other sites and match the 
density there.  Now use phenix.superpose_pdbs to find your ncs and 
put that in resolve.

Good luck!
-Tom t

At 05:48 AM 5/22/2008, you wrote:
>Apologies for the strange question.
>Since phenix has one fantastic tool for each kind of purpose, I was
>wondering if there is something that could combine features of USF
>Rave package for example.. basically the question arises from the
>difficulty of finding NCS operators in some cases, if we have less
>than three heavy atoms per molecule or map is too bad to build
>I am trying to create a mask around a heavy atom site in the map, give
>it a translation to the next heavy atom which is probably in the next
>molecule, give a 6d rotation and use that in Resolve for NCS
>Any suggestion / script would be greatly appreciated.
>Cheers, Partha
>MRC National Institute for Medical Research
>Division of Molecular Structure
>The Ridgeway, NW7 1AA, UK
>Email: pchakra at nimr.mrc.ac.uk
>Phone: + 44 208 816 2515
>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web 
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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