I do not seem to understand the meaning of fixing. Fixing something can mean
a) repairing it, implying that something was broken or amiss. Lack of experimental information expressed as omission of atoms is not something that needs fixing. b) keeping it constant. Like in having one single energy minimized conformation and accepting it once fixed as in (a). c) injection of conscience-expanding drugs, often also hallucinogenic, as in fixing in (b). d) removal of reproductive organs, as in possible punishment for mutilating experimental structure models by fixing as in (a,b,c) A discrete ensemble of probable rotamers following a distribution with constrained occupancy probabilities according to their empirically observed frequency (optimally context sensitive) might be an approximate solution to a to this date quite contentious issue. I am sure Paul will make it happen ;-) Anyhow - beware of fixers. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of debayan dey Sent: Wednesday, May 30, 2012 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] to determine missing atoms and residues in a PDB file The missing residues/atoms in the PDB file can be found out and fixed in Schrödinger program's Prime module refinement.It will automatically detect the missing atoms in a residue and will fix it. After fixing it can energy minimize it.For missing portions of residue it can build the missing portions using homology model.The other option for fixing missing atoms is to use the following server: http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php -Debayan Dey On Wed, May 30, 2012 at 5:20 PM, sreetama das <somon_...@yahoo.co.in> wrote: Dear All, I have a PDB file which does not have the REMARKS cards 465 (for missing residues) and 470 (for missing atoms). This is not a deposited PDB file. Is there any program to figure out the missing residues and atoms (some programs complain about missing atoms) ? Or do I have to check in any particular file generated during the processing of the diffraction data? The S2C program from Prof. Dunbrack's Lab does not show any option of uploading pdb files (this solution was mentioned to a previous query on the BB). Thanks in advance, sreetama -- Debayan Dey Research Fellow Dept. of Physics, Biocrystallography and Computational Biology Laboratory Indian Institute of Science India
