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Do you have the SEQRES residues? 
If these are properly generated, that should be a complete list of what is in the crystallisation, and any missing residues will just not be there in the pdb.
Any program which displays residue properties by number will show these up. Try the validation in coot - density fit option, and you should see gaps for missing residues.
Or do something like beverage, and again you will see gaps in the log graph plots.

And again coot will list missing atoms, as will REFMAC and other examples of software.

However Bernard is absolutely right - you can't "fix" these without some evidence - you probably should just note that this is the best model the authors achieved with their experimental data..
   Eleanor 


On 30 May 2012 20:40, Bernhard Rupp (Hofkristallrat a.D.) <[log in to unmask]> wrote:

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:[log in to unmask]] On Behalf Of debayan dey
Sent: Wednesday, May 30, 2012 10:59 AM
To: [log in to unmask]
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 <[log in to unmask]> 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