[ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

[Athanasios Dousis]

Hello all,

I'm forwarding a question from my labmate Hailiang Zhang regarding 
OVERLAPMAP and real-space R factors.

Thanks in advance for your suggestions.

Nasos Dousis
Rice University

P.S. Can someone please add haili...@bcm.tmc.edu to the CCP4BB listserv?

-------- Original Message --------
Subject:        calculate the real space R factor using OVERLAPMAP
Date:   Fri, 21 May 2010 17:48:47 -0500
From:   Zhang, Hailiang <haili...@bcm.tmc.edu>
To:     ndou...@rice.edu <ndou...@rice.edu>



Hi,

I wanted to calculate the real space R factor using OVERLAPMAP. According to 
the general definition of real space R value 
(http://reference.iucr.org/dictionary/Real-space_residual), everything should 
be absolute value in the formula. However, the results by OVERLAPMAP were 
giving massive negative values. I also checked OVERLAPMAP documentation and 
found that the absolute sign seems absent in the R factor formula 
)http://smb.slac.stanford.edu/facilities/software/ccp4/html/overlapmap.html). I 
was just wondering whether there is some other tools in eg CCP4, Phenix or CNS 
to calculate real-space R in the general way in absolute values.

Thanks!