Here we go again! We neither have evidence that some mysterious side-chainnase has chopped off all flexible surface side chains and in fact, at least I am pretty sure these side chains are still there and moving around in the solvent as indicated by their very/extremely high B-factors, which, again for me, is the better description of the "real" situation.
My 2 cents! Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Thursday, March 01, 2012 3:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Temp Fact Variance Analysis -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Ros, yes, the lack of electron density is most likely the cause the these red bars (unless you set the map level rather high, but at the default chosen by coot that should be fine). yes - if you don't see electron density you don't have experimental evidence of the atom positions, so it is best to delete them. Tim On 03/01/2012 03:26 PM, Uma Ratu wrote: > Hello, > > I run my model in Coot to do "Temp Fact Variance Analysis". > There are red bars from the B-factor Variance graphy. > I click each red bar to exam the residues in Coot. Many of these > residues do not have the electronic density on their side chains, > especially Lys residues. > > Here is my questions: > > 1. The lack of electronic density is the cause of these red-bars? > 2. How do I fix them? delete the side chains? > > The diffraction data is 2A, and data completness is 98.8%. > > Thank you for comments > > Ros > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPT4qVUxlJ7aRr7hoRAqpPAKDhbjhjlU61IKVWJRqtMWNRrmv9mQCg9bVV ksQAnMWWcUyA9xvptO6mnlk= =iaww -----END PGP SIGNATURE-----
