creating mask from a map

Dear Members,

If I don't have any known homologous structure, how can I make a mask from a manually refined map? I have now 6.9A map created by manual refinement in cistem. I like to do sharpen with mask. Can someone give any hint?

Thanks,

Raj

Hi Raj,

For my masks, I use the method I described here :-

https://cistem.org/manual-refine

Thanks,

Tim

Hi Tim,

Thanks for the link. I actually tried similar way. But sharpen 3D did not improve the map quality. As I don't have any structural information, don't know how to check the reliability of the map I created in cistem. Any suggestion would be very helpful.

Thanks,

Raj

Hi Raj,

Do you see clear alpha helices?

You definitely should at 7A.

Tim

Hi Tim,

Is it possible to sort particles by ctf-Max-resolution or FOM in cistem?

Thanks,

Raj

Hi Raj,

You cannot directly sort particles this way, you can sort / select images into a group. Then use that group to select only particles from those images.

Tim

Could you please check if I

Could you please check if I send you the mrc file to the email: tim@tgrant.co.uk (or any other e-mail address) ?

Thanks,

Raj

Hi Raj,

If you have to send it to me, that probably means you don't see helices? I take it there is no known structure of any part?

Tim

Hi Tim,

I can see some helical features, but not very clear. This is 182Kd protein monomer. Only about 360 residue (out of 1800 redue long protein) close to N-terminal is known by x-ray. I have clear 2d class-averages with about 150k particles. I really need some help from expart people like you to improve the map, so I can build the model. Don't know what to do at this point. If you are interested, I can communicate with your personal e-mail sending some files to have a look.

Thanks for your time,

Raj