[ccp4bb] structure validation tools
Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] structure validation tools
Dear Katja, I find the Molprobity server very useful. It analyses key factors of your structure like Ramachandran plot, rotamer outliers or clashes and tells you where improvements are necessary. It also ranks your model in respect to other structures in the pdb of similar resolution which gives you some idea how much you still have to work on it. Of course it will stay a bit of a subjective decision when to stop refinement but this may help you make this decision. Good luck, Joerg http://molprobity.biochem.duke.edu/ On 21 Oct 2009, at 14:20, Katja Schleider wrote: Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com *** Dr Jörg Standfuss Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH
Re: [ccp4bb] structure validation tools
Hi Katja, a possible option: from main PHENIX GUI select Comprehensive validation. For example, it will do: - all Molprobity checks; - draw POLYGON picture (Acta Cryst. D65, 297-300 (2009) Crystallographic model quality at a glance.); - show all kinds of stereochenistry rmsds; - real-space correlation coefficient computed per residue or atom, and more. Pavel. On 10/21/09 6:20 AM, Katja Schleider wrote: Hi everybody, I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? I found several validation tools in coot, but I would like to be sure on what I have to emphasize. Thank you very much in advance, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] structure validation tools
On Wed, Oct 21, 2009 at 6:20 AM, Katja Schleider katjaschlei...@yahoo.dewrote: I solved my first crystalstructure and now want to publish it. But how do I know the structure is ready for publication and deposition in the pdb. We can explain our theory with the structure but which factors I have to regard to publish nothing wrong or bad. Can anybody tell how many outliers are allowed as long as they are in a well defined density? The Molprobity server suggests the following: 0.2% Ramachandran outliers 98% Ramachandran favored 1% Rotamer outliers 1% of residues with bad bonds 0.5% of residues with bad angles (and the clashscore should be as low as possible.) -Nat
