phenix.resolve_cryo_em resolution and real space refinement
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: [email protected]
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)
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: [email protected]
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-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010
Hi Tom,
Thanks very much for the clarification!
Best wishes
Dave
From: Tom Terwilliger
participants (2)
-
David Lawson (JIC) -
Tom Terwilliger