[ccp4bb] Research Scientist at Hauptman-Woodward Institute

Please see the posting below for an independent investigator at the Hauptman-Woodard Institute. Please direct any questions or applications to the opportun...@hwi.buffalo.edu email address. Best wishes, Andrew -- Andrew M. Gulick, Ph.D.

[ccp4bb] Research Scientist at Hauptman-Woodward Institute, Buffalo, USA

Please see the posting below for an independent investigator at the Hauptman-Woodard Institute. Please direct any questions or applications to the opportun...@hwi.buffalo.edu email address. Best wishes, Andrew -- Andrew M. Gulick, Ph.D. - Hauptman-Woodward

[ccp4bb] Assistant Professor Opportunity at FSU

Dear colleagues, I am writing to draw your attention to a new Assistant Professor faculty position at FSU. The Department of Chemistry and Biochemistry at Florida State University seeks to fill a tenure-track faculty position at the Assistant Professor level in the area of biochemistry,

Re: [ccp4bb] NMR or Homology Model as a MR model

Percent of identity/similarity is a number that might be often misleading when used as a judgement rule for molecular replacement. Very high or very low numbers are almost always indicative of corresponding outcome. The numbers in twilight zone of 20 to 35%, however, are not. When aligning

Re: [ccp4bb] CC(1/2) reference

Hi Nicola, maybe you want to have a look at an older thread I started years ago: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28031.html [ccp4bb] CC1/2, XDS and resolution cut off - The Mail Archive

Re: [ccp4bb] CC(1/2) reference

Dear Nicola the most thorough discussion I have seen regarding recommendations on cutoffs (or at least ways to think about them) for such crystallographic data indicators can be found in: Assessing and maximizing data quality in macromolecular crystallography P Andrew Karplus and Kay Diederichs

Re: [ccp4bb] CC(1/2) reference

Hi Nicola, Here are references for CC1/2; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ Best Wishes Partha On Tue, Aug 29, 2017 at 10:06 AM Nicola Evans wrote: > Hello all, I have heard at several CCP4

[ccp4bb] CC(1/2) reference

Hello all, I have heard at several CCP4 meetings and also at Diamond training that a good "cut off" for CC(1/2) is around 0.3 and I/sig(I) is 0.2, but I am struggling to find any journal references to say this (other than demonstrating the merits of CC(1/2) over Rmeas). Can anyone point me in

Re: [ccp4bb] NMR or Homology Model as a MR model

Hi Nishant AMPLE can work with ensembles from NMR structures (http://ample.readthedocs.io/en/latest/examples/rst/nmr_ensemble.html#example-nmr-ensemble; see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817692/) or sets of distant homologues

Re: [ccp4bb] NMR or Homology Model as a MR model

Hi, Molecular replacement gets progressively more difficult as the sequence identity drops, though the correlation between sequence identity and model quality is not perfect. With the best models having sequence identities around 24%, success is by no means guaranteed, so you might have to

Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant, For successful MR a choice of domain boundaries and loop trimming is crucial. Last couple of years I do not even try to run molrep/phaser before running MrBump and Morda, which do a good job with model preparation. Only when these pipelines give leads, but not quite the results I

Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant, Rosetta is a good suggestion. You can also use an ensemble of several related (superposed) structures as your search model. This will improve your chances of success. All best. Andreas On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney wrote: > Dear

Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant, You can use anything you want as a molecular replacement search model including NMR models/ensembles or homology models. Whether or not it will be successful is another matter! For borderline cases, some have reported success using Phaser in combination with the Rosetta

[ccp4bb] NMR or Homology Model as a MR model

Dear Crystallographers, I am working to solve an human protein structure which has a domain sequence identity of 24% with domain of another protein. As Phaser as well as Molrep failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if solution structure of another protein having