Re: [ccp4bb] Deletion of hydrogens

Reduce also has an option to remove hydrogens at the command line. [phenix.]reduce -Trim model.pdb Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email :

[ccp4bb] Deletion of hydrogens

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

Re: [ccp4bb] Deletion of hydrogens

-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

Re: [ccp4bb] Deletion of hydrogens

On 19/05/15 11:55, 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? This will create a new molecule that is a copy of

Re: [ccp4bb] Deletion of hydrogens

Dear Mohammad, You can use 'modify pdb' tool in phenix utilities and select remove hydrogen option. Also, if you are familiar with Vim editor in linux then there is easy command (:g/ H/d). Regards, NIKHIL G BHARAMBE, Ph.D Student, Prof. K. Suguna's Lab Molecular Biophysics Unit (MBU)