Re: [ccp4bb] building into EM map

2018-01-24 Thread Martyn Winn 
You could look at the CCP-EM software http://www.ccpem.ac.uk/download.php which 
includes CCP4 programs adapted to cryoEM (e.g. allowing input of cryoEM map).

There is a range of possibilities from rigid body fitting of components, 
flexible fitting or de novo building.  At 4 A, you may struggle with de novo 
building, though of course you may have regions where the local resolution is 
better.

There are some tutorials etc here 
http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

Good luck
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Natalia O
Sent: 23 January 2018 20:04
To: ccp4bb
Subject: [ccp4bb] building into EM map

Hello,

I am new to building into an EM map, and I wonder if I could get a 
recommendation for some standard routine for programs to use. I tried "find 
helixes and strands" tool in phenix, it found some secondary structure 
elements, however, it seems that there is more that could be done 
automatically. Is there any standard set of tools to use for automatic building 
in EM map of about 4A resolution?

Thank you!

-Natalia

Re: [ccp4bb] building into EM map

2018-01-23 Thread Pavel Afonine 
> I am new to building into an EM map, and I wonder if I could get a
> recommendation for some standard routine for programs to use. I tried "find
> helixes and strands" tool in phenix, it found some secondary structure
> elements, however, it seems that there is more that could be done
> automatically. Is there any standard set of tools to use for automatic
> building in EM map of about 4A resolution?
>


phenix.map_to_model may be able to do more:
https://www.phenix-online.org/documentation/reference/map_to_model.html

Pavel

[ccp4bb] building into EM map

2018-01-23 Thread Natalia O 
Hello,

I am new to building into an EM map, and I wonder if I could get a
recommendation for some standard routine for programs to use. I tried "find
helixes and strands" tool in phenix, it found some secondary structure
elements, however, it seems that there is more that could be done
automatically. Is there any standard set of tools to use for automatic
building in EM map of about 4A resolution?

Thank you!

-Natalia