-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Salut Xavier,
(i) you have to give the explicit residue range when changing the chain ID. The 'whole chain' does not work. (ii) Renumber the downstream end by adding one, and add the residue (iii) Under Edit->Preferences->Others->Fonts you can choose "Larger" (iv) I don't know Best, Tim On 03/22/2013 04:16 PM, "F.Xavier Gomis-Rüth" wrote: > Dear Paul & The Cooters, > some questions: > (i) Is it possible to tell the program in a rather straightforward manner to > connect two chains within a model > that have different chain identifiers? This is very useful when rebuilding > models created by automatic tracing > programs. I also found that manual renaming of a chain to match another > letter > doesn't work if this letter is already > taken by another chain. > (ii) If I understood it correctly, the program only adds residues to termini. > How do I "insert" a residue between two > residues of a chain with correlative numbering? > (iii) Can I put larger larger labels and numbers? Specially when working in > Zalman stereo mode, the numbers are really small... > (iv) How do I remove alternate conformations without deleting the residue and > inserting a new one manually? > Thanks a lot in advance, > Xavier > > > On 8/3/13 3:20 PM, Paul Emsley wrote: >> On 07/03/13 12:27, Dave wrote: >>> Hi - >>> >>> I'm working on a mammalian derived crystal. In a few chains where I can see >>> the N-terminus, it appears that they are acetylated. I looked for previous >>> discussion on how to deal with this, and I was wondering how exactly to >>> deal >>> with this in coot as of 2013. >>> >>> Thus far, I added an ala to the n-terminus, then used >>> extensions>modelling>replace residue >>> to mutate to ACE >> >> That sounds fine. >>> >>> I'm running coot 0.7 stable release sept 2012. >>> >>> I'm not seeing a bond between the original N-term N atom and the C of he >>> acetyl group >> >> Coot won't link het groups that are non-polymers. Maybe there should be an >> exception for ACE. >> >>> >>> Real Space Refine Zone and Regularize Zone do not like the setup. >> >> quite right. >> >>> I'm sure I need to define some things, but haven't dealt with this before, >>> as >>> for things like this, I used to switch to xfit. >> >> :-( >> >> I suspect that you need to not tell coot that ACE is a non-polymer - you can >> do that by either copying and hand-editing the cif file or using Edit -> >> Restraints -> ACE -> then change "non-polymer" to "L-peptide", Apply. >> >> Then I would do a sphere refine. >> >>> >>> Would it be better to ask at CCP4? >>> >> >> :-( >> >> >> Paul. >> > > -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRTNOzUxlJ7aRr7hoRAgCmAKDIK/xznI7ZoSFucWo0hJF0XUGOmwCbBx0Q qZkMRRQs3z48sdPVP7YdXhA= =H4J1 -----END PGP SIGNATURE-----
