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Jian,
I have addressed the same query before in excruciating detail. Correct
specifications like Kevin points out could fix your problem.
Visit
http://groups.yahoo.com/group/cnsbb/message/818
for the details
Raji
On Dec 5, 2005, at 12:18 PM, Kevin Jude wrote:
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Refinement of multiple conformations in CNS isn't very straightforward,
so I try to save it
until the end of refinement. You probably forgot to edit your
refinement input files to tell
them that you have multiple conformations, eg:
{* select atoms in alternate conformation 1 *}
{===>} conf_1=(segid AC1);
{* select atoms in alternate conformation 2 *}
{===>} conf_2=(segid AC2);
hope this helps,
kmj
Jian Wu wrote:
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Hello everyone:
Now I am refining a set of low-resolution data which contains my
enzyme,
an acyl-CoA and a drug and all is OK for the protein and the acyl-CoA.
But the modest density indicates that the drug maybe exist with dual
conformtions and the pocket nearby accomodate enough space for the
drug
to convert from one conformation into another.
Using the "alternate.inp" in CNS, I generate the coordinate file and
structure file and then adjust the two conformers to the 'correct
places'. However, the two conformers locate near to each other and
have
an overlapping hexacyclic ring. So when I want to refine it in CNS, it
tell me that the two conformers have conflicts on the hexacyclic rings
and automatically 'push' them out from the density. : (
I am wondering if you guys have the similar experience. Any suggestion
and comments are welcome!
Thanks in advance!
--
Jian Wu
Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)
Tel: 0086-21-54921117
Email: [EMAIL PROTECTED]
