All right let me know if anything performs better than phenix.real_space_refine and I will do my best to catch up -;) Pavel P.S.: phenix.real_space_refine is still under active development. On 7/28/14, 9:31 AM, George Devaniranjan wrote:

Hi Pavel,

Thank you, I have also tried COOT but I wanted to know whether anyone had used (with success ) other similar tools.

Why? Mostly curiosity :) but also to do a comparison I guess of performance.

Thank you, I will check some of the others you have mentioned.

George

On Mon, Jul 28, 2014 at 9:29 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi George,

as far as I know phenix.real_space_refine is the only user-exposed real-space refinement utility in Phenix. You can think of Tom's morphing as a kind of real-space refinement (phenix.morph_model). Also, you can think of mmtbx.lockit as a simplest version of phenix.real_space_refine.

Outside Phenix I would say Coot, Chimera, HermiteFit, ... there are many more and Google is your friend to find them.

Just curious: why?

Pavel

On 7/28/14, 9:19 AM, George Devaniranjan wrote:

...

Hi,

I know this is going to sound blasphemous in phenix (my apology particularly to Pavel) but is there other s/w that does similar things to phenix.real_space_refine ?

I used that already (works very well) but was wondering if there was anything similar out there to do a comparison.

Thank you, George

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It is unique in a sense that it is closest to Bob Diamond's original work (197?), and also it uses LS=SUM(rho_obs-rho_calc)**2, where rho_calc is resolution truncated analytical density function originally developed by Michael Chapman and published I guess in 1995. More details: http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf pages 37-40. Pavel On 7/28/14, 12:17 PM, Nathaniel Echols wrote:

On Mon, Jul 28, 2014 at 12:12 PM, Tim Gruene mailto:[email protected]> wrote:

- - Michael Chapman's RSRef (http://www.sb.fsu.edu/~rsref/Distribution/software_distribution.htm http://www.sb.fsu.edu/%7Ersref/Distribution/software_distribution.htm)

Argh, forgot to mention this! That's probably the closest analogue, although I don't think it does local refinement (i.e. sidechain fitting), does it?

-Nat

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