Hello, I have a question on refinement of macromolecules. I like to apply 180 degree rotation to the side chain of a particular residue about a particular bond and see, which one (before or after applying rotation) agrees well with the observed x-ray data (based on R factors and electron density map). Can someone advise, what could be the best way to do this? I like to do the same operation on multiple structures which are already refined. Regards, hena
Hi Hena, the answer to your question: http://phenix-online.org/pipermail/phenixbb/2011-February/005316.html This should be available in *development* version of PHENIX, dev-673: http://www.phenix-online.org/download/nightly_builds.cgi?show_all=1 which is not officially released. You can do it in Coot too. Let me know if you have any questions. Pavel. On 2/18/11 9:12 AM, Hena Dutta wrote:
Hello,
I have a question on refinement of macromolecules. I like to apply 180 degree rotation to the side chain of a particular residue about a particular bond and see, which one (before or after applying rotation) agrees well with the observed x-ray data (based on R factors and electron density map). Can someone advise, what could be the best way to do this? I like to do the same operation on multiple structures which are already refined.
Regards,
hena
Hi all How many cycles are required to remove the Rfree bias for different R-free data set. I usually do annealing at CNS. For the different Rfree set, I used to give 5 or 10 cycles of refinement, but Rfree varies between 2% between the cycles. I like to know that just adp refinement or annealing_torsion is required for different R-free set? How many cycles will be sufficient to remove rfree bias? Thanks Ram
Hi Ram,
How many cycles are required to remove the Rfree bias for different R-free data set. I usually do annealing at CNS.
- slightly shake coordinates and ADPs; - remove water (if present); - run phenix.refine with or without SA, refine coordinates, B-factors, use automated water update option, as many macro-cycles as necessary to achieve convergence (for example, R-factors stop changing). Alternatively, you may consider running your model through phenix.autobuild (which will be more thorough but time consuming option). The above strategy may (significantly) vary depending on the data resolution. Pavel.
participants (3)
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Hena Dutta -
Pavel Afonine -
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