Re: [COOT] merge symmetry related atoms in coot
This is tricky I find .. You can use the NCS ghost to fit the bits of A you like over B, then work out what bits of B you want to shift into A. There are tools to rename that bit of B to A and if necessary renumber it as well.. Then output the renamed file and you will probably have to edit it by hand to get the fragments in the right order.. Eleanor jenny flower wrote: Hello I have a partial model with 4 chains, but some part of A chain is in B chain, can I merge the symmetry related atoms to make a right A chain? thanks Qing Chen
Re: [COOT] to regenerate a pdb file from ssm matrix
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]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#SEC134http://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.
Re: [COOT] to regenerate a pdb file from ssm matrix
Dear Qing Chen, Woops, sorry - the documentation is out of date - I'll fix it shortly.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.
Re: [COOT] to regenerate a pdb file from ssm matrix
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#SEC134http://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.
