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 : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, May 19, 2015 at 8:49 AM, Nikhil Bharambe nikh...@mbu.iisc.ernet.in wrote: 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) IISc, Bangalore. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[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 maybe slowing down the process. Thank you Mohammad
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 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-
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 molecule number 0 without hydrogens: (new-molecule-by-atom-selection 0 //*//*[!H]) Moreover, if I do my refinemnets with hydrogens in it, will it affect my results, other than maybe slowing down the process. If you use hydrogens in refinement then no (or not much). Paul.
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) IISc, Bangalore. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
