-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Mohammad,
you can use e.g. the CCP4 tool pdbset with its keyword 'EXCLUDE HYDROGENS'. You could also repeat the refmac run but ask refmac not to include the hydrogen atoms in the output PDB. This is the default and available as option from the ccp4 GUI. I don't know how to steer this from Coot, though. You should always include hydrogen atoms during refinement. They improve the geometry restraints and they also have a small contribution to the X-ray scattering, especially at low resolution. Given their number approximately equals that of all other atoms in your structure, this small contribution may add up. You probably won't notice much of a slow down by including hydrogen atoms during refinement. There are probably other bottlenecks. Regards, Tim On 05/19/2015 12:55 PM, Mohammad Khan wrote: > Dear all, > > I have added hydrogens on my molecule using the Refmac option in > Coot. I now want to remove them. I tried various syntax but they > didn't work. Is there a simple way to remove them from the pdb? > > Moreover, if I do my refinemnets with hydrogens in it, will it > affect my results, other than maybe slowing down the process. > > Thank you > > Mohammad > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVWxtcUxlJ7aRr7hoRAgbGAJwJ24mkNXdBCkOiQ8angknihROamwCeLHTc lH3eHumFsNpBcsP2Q+xpbIE= =tAwF -----END PGP SIGNATURE-----
