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missing residues in pdb file

missing residues in pdb file - Protein Forum

missing residues in pdb file - Protein Forum


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Old 07-04-2008, 04:56 AM
ozgun.harmanci
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Default missing residues in pdb file



Hello,
I am having trouuble with missing residues in pdb files and need to
replace them (i.e. interpolate them) using a program. I think swiss-
pdbviewer and pymol do that. My problem is that I am not very capable
of using those programs and the person whom I asked for help told me
that I have to check for missing residues in pdb file, open swiss-
pdbviewer then add residue at correct place and finally she told me
that I might need to do an energy minimization and I am thinking that
I will definitely do a mistake there. I was wondering if anyone knows
a more automated way to get the missing residues inserted for me
because I am thinking that you can find missing residues in pdb and
and programs can read that info and add these missing residues
themselves automatically.. (but again maybe not..)

Thanks.

Sincerely,
Arif.
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Old 07-07-2008, 03:54 PM
DK
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Default missing residues in pdb file

In article <[Only registered users see links. ]>, "ozgun.harmanci" <[Only registered users see links. ]> wrote:

Missing residues mean that they were too flexible in the crystal to be
detected by X-ray scattering. Which, crudely, means that they were
"everywhere". So just add the residues manually into some random
non-folded conformation avoiding close contacts with the rest of
the protein.

But keep in mind that in reality you don't know where these residues
really are => the new positions you built should not form a basis
for any analysis/results. In that respect, you will probably be better
off not building any missing residues into your PDB at all.

DK
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