Hi Paul,
I could not find NCS copy chain function under my coot 0.4.1. I was trying to update my coot using fink, but failed. So I did it in a maybe unusual way: 1, I use SSM superinpose my A chain to B, C, D, accoring to the rotation and translation matrix I got from coot , I run pdbset to creat chain B,C,D from rebuilt-A chain one by one 2, then I open chain A and converted chain B,C,D in coot again and merged then It is a bit labourious..... thanks! Qing On Mon, Aug 11, 2008 at 4:15 PM, Paul Emsley <[EMAIL PROTECTED]>wrote: > > 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 Woops, sorry - the documentation is out of date - I'll fix it shortly.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> >> < >> 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. >> >> >> >
