Re: [ccp4bb] to determine missing atoms and residues in a PDB file
Hi Eleanor, was there recently an update to beverage ? Could you send me a link to version 2.0 perhaps ? And more importantly it hopefully was compiled with EtOH and some vitamins :-) Jürgen On May 31, 2012, at 7:02 AM, Eleanor Dodson wrote: Or do something like beverage, and again you will see gaps in the log graph plots. Eleanor .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] to determine missing atoms and residues in a PDB file
sreetama das 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 I think if you generate SEQRES records for the sequence of your protein (or grab them from another pdb if another structure has been deposited), add them to your raw pdb, and submit to the validation server at the PDB, the validation report will include detailed listing of missing residues and missing atom in partial residues.
Re: [ccp4bb] to determine missing atoms and residues in a PDB file
On 30/05/12 12:50, sreetama das 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). The fill-partial-residues function or the Rotamer probability validation tool in Coot will find standard residues with missing atoms.
Re: [ccp4bb] to determine missing atoms and residues in a PDB file
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
