Re: [COOT] to regenerate a pdb file from ssm matrix

2008-08-11 Thread Qing Chen
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 crea

Re: [COOT] to regenerate a pdb file from ssm matrix

2008-08-11 Thread Paul Emsley
Dear Qing Chen, Woops, sorry - the documentation is out of date - I'll fix it shortly.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 c

Re: [COOT] to regenerate a pdb file from ssm matrix

2008-08-11 Thread Qing Chen
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 tho

Re: [COOT] to regenerate a pdb file from ssm matrix

2008-08-10 Thread Paul Emsley
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 infor