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 already seen EPMR handle some Hydrogen as Carbon,
I am ready to see anything happening! :(
I will have a quick look to see if I can make Phaser
output atom numbers from what was read from the PDB.
Regards,
F.
Regards,
Markus
On Tue, 12 Jan 2010, Francois Berenger wrote:
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
1 6.9 9.6 7.0 9.4
2 5.2 5.9 5.4 6.2
3 4.2 4.5 4.7 5.2
4 4.9 6.8 5.2 6.7
Hence, here are my existential questions, given that I heard
many times "H is transparent for X-rays":
* should I always remove H before running Phaser?
* why?
Here are a few lines of one of my PDBs containing H, in case it is
misinterpreted by Phaser:
---
ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00
ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00
ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00
ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00
ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00
ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00
ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 ---
Thanks a lot,
Francois.
