Hi,

Probably your mask is too tight.
Make sure you have applied low pass filtering (15 A is a
good value) and added wide soft edges in the MaskCreate job.

 > nominal resolution of 3.3A

Please also examine the FSC table in run_model.star from Refine3D.
Refine3D reports the highest resolution where FSC crosses 0.143,
while Postprocess reports the lowest resolution where FSC crosses 0.143.
So, if you have a dip and bump in the FSC curve, Refine3D and
Postprocess might report different resolutions.
(see an example in 
https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Pixel_size_issues. 
This can be caused by
errors in pixel size, beam tilt, defocus, etc.)

Best regards,

Takanori Nakane

On 2018/12/07 20:32, Pranav Shah wrote:
> Dear Sjors and Team,
> 
> I have refined a map to a nominal resolution of 3.3A and wish to B-factor
> sharpen the map. I generated a mask with the following params
> 
> which relion_mask_create` --i Refine3D/job133/run_class001.mrc --o
> MaskCreate/job138/mask.mrc --lowpass 15 --ini_threshold 0.019
> --extend_inimask 5 --width_soft_edge 5 --j 5
> and checked if the mask encloses the capsid density (see attached)
> [image: Screen Shot 2018-12-07 at 3.32.03 PM.png]
> I executed the post-process job with the default options which ran to
> completion but with the following error
> 
> WARNING: the unmasked FSC extends beyond the solvent-corrected FSC. Skip
> masking for now, but you may want to adjust you mask!
>            You can force the mask by the '--force_mask' option.
> 
> and the reported resolution was degraded to 6.1 instead of going higher.
> 
> Could you explain what the cause of this error is and what steps i need to
> take to prevent this from happening again?
> Cheers,
> Pranav
> 

########################################################################

To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1