Dear Qing Chen,
Woops, sorry - the documentation is out of date - I'll fix it shortly.
The copy chain makes exact copies of the master chain (with the NCS
transformation applied obviously).
Which means of course, mutations, deletions, insertions will be applied too.
I have added a NCS copy chain function to Extensions as of revision
1327. That should help.
Paul.
Qing Chen wrote:
Hello Paul,
Yes, I did some model building using Coot only of chain A. I checked the
link, it is saying:
Note that you can currently only apply NCS edits to residues that exist
in the "other" chains. If for example, you had introduced/added residues
1 to 5 in the "A" chain and wanted to copies those over to the other
molecules, then that would not work (88)
<http://www.ysbl.york.ac.uk/%7Eemsley/coot/doc/chapters/user-manual_fot.html#FOOT88>.
Since I did renumbering, adding ,deleting residues to chain A, so seems
it wouldnot work by apply NCS. Now I would like to run refmac5, so I
need a complete model, right?
I am a rather beginner, is there any better ways to rebuild in my case(4
molecules in one assymetry unit).
thanks
On Sun, Aug 10, 2008 at 9:36 PM, Paul Emsley <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
jenny flower wrote:
Hello,
I have 4 chains in my pdb, I SSM chain B,C,D to chain A. If I
refined chain A, can regenerate a pdb with whole 4 chains from
refined chain A, by applying SSM matrix? I see Xterm window show
SSM matrix when I do SSM, but somewhere a log file contain this
matrix information also?
Dear Qing/Jenny Flower,
When you say "I refined chain A", I am presuming that you mean that
you have done some model building using Coot. You then want to
apply the edits that you have made each of the chains in your model
(applying the NCS transformations as necessary):
You should read the user manual, section 5.27 Applying NCS Edits:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC134
<http://www.ysbl.york.ac.uk/%7Eemsley/coot/doc/chapters/user-manual_5.html#SEC134>
In your case it seems that you want this function:
(copy-from-ncs-master-to-others imol master-chain-id)
HTH,
Paul.
