[phenixbb] phenix.resolve_cryo_em resolution and real space refinement

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Wed Oct 14 04:51:53 PDT 2020


Hi Dave,

Yes, the 7.08 in:

d-values (A)

where

FSCref=0.5:   7.08    6.69    6.63


Is referring to the estimated initial resolution where the half-dataset
correlation is 0.143, leading to an estimated correlation to the true map
of 0.5.   The 6.69 number is the map-phasing map, and the 6.63 is the
density modified (combined) map.


Yes, the density modification resolution limit is chosen empirically as a
finer resolution than you supply as a nominal resolution.


I think that your real-space refinement correlations won't be very
different if you use 7.1 or 6.6 A as your nominal resolution.  I'd suggest
using the estimated resolution from density modification but it may be more
important to be consistent with other runs if you want to compare results.


All the best,

Tom T

On Wed, Oct 14, 2020 at 5:29 AM David Lawson (JIC) <david.lawson at jic.ac.uk>
wrote:

> Hi All,
>
>
>
> I have run phenix.resolve_cryo_em using half maps at 7.5 A resolution (the
> postprocessed map is at 7.1 A) and I just wanted to clarify a couple of
> things (I have pasted the end of the logfile below this message). I set the
> resolution to 7.52 A but didn’t supply a resolution for density
> modification – it seems to have chosen a value of 5.671 A
>
> (1) It states “Estimated improvement of -0.450 A to  d_min(FSCref=0.5):
> 6.628 A” suggesting to me that it agrees with the postprocessed resolution.
> Is this the value of 7.08 on this line: “FSCref=0.5:   7.08    6.69
> 6.63”?
>
> (2) I understand that the actual process of real space refinement doesn’t
> care about the resolution of the map, but you need to supply it to get
> meaningful CC values. So my question is what resolution should I supply to
> RSR if I use the density modified map?
>
>
>
> I realise that a value of “-0.450 A” is at the upper end of what to expect
> from density improvement, but I can report that the DM map does look
> noticeably better than the postprocessed map, especially in regions that
> are less well defined.
>
>
>
> Many thanks in advance for any advice
>
>
>
> Dave Lawson
>
> -----------------------------------
>
> d-values (A)
>
> where
>
> FSCref=0.5:   7.08    6.69    6.63
>
>
>
> Estimated improvement in d_cc_star=0.5: -0.450 A
>
>
>
> This is new current best working_map_coeffs_info. Estimated
>
> improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A
>
>
>
> Done testing....R-value: 0.530  Try: 1 ['database 5', 'resolution: 5.67 ',
> 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False',
> 'apply_cc_star:True', 'b_iso: None A**2']
>
>
>
> Best density modification cycle 1 is try 1 with
>
> Methods used: ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ',
> 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None
> A**2']
>
> R-value: 0.530
>
> Estimated improvement of -0.450 A to  d_min(FSCref=0.5): 6.628 A
>
> Result: -0.450 A to d_min(FSCref=0.5): 6.628 A  R-value: 0.530
>
>
>
> Wrote working map to /home/lawsond/phenix/ResolveCryoEM_1/map_denmod.ccp4
>
>
>
>
> ===============================================================================
>
> SUMMARY AFTER CYCLE OF DENSITY-MODIFICATION
>
>
> ===============================================================================
>
>
>
>
>
> Overall best density modification Cycle 1 try 1
>
> Estimated improvement: -0.450 A to d_min(FSCref=0.5): 6.628 A   R-value:
> 0.530
>
> Denmod resolution: 5.671 A
>
> Database: 5.000 A
>
>
>
> Writing out final map files…
>
>
>
> -------------------------------
>
> Prof. David M. Lawson
>
> Department of Biological Chemistry,
>
> John Innes Centre,
>
> Norwich,
>
> NR4 7UH, UK.
>
> Tel: +44-(0)1603-450725
>
> Web: https://www.jic.ac.uk/people/david-lawson
>
> Email: david.lawson at jic.ac.uk
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org



-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20201014/3c351ca1/attachment-0001.htm>


More information about the phenixbb mailing list