Re: [ccp4bb] Copy NCS chain in coot
Dear Zhang yu, I also found that same problem recently. I think is a small bug from Coot. It will only copy NCS if the molecule's name you want to copy is molecule A. So maybe will work if you rename your built chain as A. Good luck! Javier On 31/03/11 00:16, zhang yu wrote: Dear all, I have two fold NCS in ASU. I could find phase by molecular replacement, but I have to build other chains by myself, since the model is not complete. During model building in coot, I built one chain in one NCS, and I merged this chain into the previous molecule. Now it is the chain M'. When I tried to directly copy this chain to its NCS mate, It didn't work. I followed the instruction posted beforehttp://www.mail-archive.com/coot@jiscmail.ac.uk/msg01984.html;. What I did is 1. Change the master chain to chain M Draw-NCS ghost control-change to chain M (The terminal said 'there are no ghosts when I change the master chain to chain M) 2. go to Extension-NCS-copy chain-, coot ask to fill the master chain ID, and I typed M Nothing happened. Could someone tell me what is the correct procedure to do it ? Bye the way, for those chains present in both NCS maps, I modified one chain and applied the change to its NCS mate by using the same above procedure, and it worked. Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Copy NCS chain in coot
Dear Javier, Thanks for your reply. I am using coot 0.6.1, and I could copy molecules with names besides A only if chains are already present in both NCS. For chains which are only present in one NCS , I did find out a way to copy to the other NCS by using 'Find NCS ligand' , although it is not a ligand. For example, there are already chain A - chain D in the first NCS, and chain E-chain H in the second NCS. I build chain 'M' from the scratch in the first NCS, and I want to copy it to its NCS mate. 1. Change the master chain to chain A Draw-NCS ghost control-change to chain A 2. go to Extension-NCS-NCS ligands-, In upper dialog box, Protein with NCS, Fill the master chain ID to A. In the lower dialogue box Molecules contain ligands, choose the right molecule and Fill 'M' and 'residue ranges'. Coot will give a few positions to fit the chain, just choose the right one. Yu 2011/3/31 Javier Garcia gar...@ysbl.york.ac.uk Dear Zhang yu, I also found that same problem recently. I think is a small bug from Coot. It will only copy NCS if the molecule's name you want to copy is molecule A. So maybe will work if you rename your built chain as A. Good luck! Javier On 31/03/11 00:16, zhang yu wrote: Dear all, I have two fold NCS in ASU. I could find phase by molecular replacement, but I have to build other chains by myself, since the model is not complete. During model building in coot, I built one chain in one NCS, and I merged this chain into the previous molecule. Now it is the chain M'. When I tried to directly copy this chain to its NCS mate, It didn't work. I followed the instruction posted before http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01984.html;. What I did is 1. Change the master chain to chain M Draw-NCS ghost control-change to chain M (The terminal said 'there are no ghosts when I change the master chain to chain M) 2. go to Extension-NCS-copy chain-, coot ask to fill the master chain ID, and I typed M Nothing happened. Could someone tell me what is the correct procedure to do it ? Bye the way, for those chains present in both NCS maps, I modified one chain and applied the change to its NCS mate by using the same above procedure, and it worked. Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] Copy NCS chain in coot
Dear all, I have two fold NCS in ASU. I could find phase by molecular replacement, but I have to build other chains by myself, since the model is not complete. During model building in coot, I built one chain in one NCS, and I merged this chain into the previous molecule. Now it is the chain M'. When I tried to directly copy this chain to its NCS mate, It didn't work. I followed the instruction posted before http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01984.html;. What I did is 1. Change the master chain to chain M Draw-NCS ghost control-change to chain M (The terminal said 'there are no ghosts when I change the master chain to chain M) 2. go to Extension-NCS-copy chain-, coot ask to fill the master chain ID, and I typed M Nothing happened. Could someone tell me what is the correct procedure to do it ? Bye the way, for those chains present in both NCS maps, I modified one chain and applied the change to its NCS mate by using the same above procedure, and it worked. Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
