[ccp4bb] Phaser: removing H in PDB increases the RFZ ?!

2010-01-12 Thread Francois Berenger
Hello, I have 4 molecules. If I use Phaser's AUTO_MR with all default parameters on them, I get the following scores: no_modif remove_H molecule RFZ TFZ RFZ TFZ 16.9 9.6 7.0 9.4 25.2 5.9 5.4 6.2 34.2 4.5 4.7 5.2 44.9 6.8 5.2 6.7 Hence, here are my

Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!

2010-01-12 Thread Eleanor Dodson
Just to avoid any problem pdbcur xyzin X.pdb xyzout X-nohyd.pdb DELHYD END Eleanor Francois Berenger wrote: Markus Rudolph wrote: Hello, long ago I had a case when HG1 etc. were interpreted as mercury by phaser. Could that be relevant to your case? I hope not. However, as I have

Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!

2010-01-12 Thread Ed Pozharski
The increase in RFZ is relatively small and not entirely unexpected. While hydrogens only contribute one electron (as opposed to carbon (6), nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in fact, almost as many as all the other atoms combined). For instance, in lysozyme you