Re: altering residues in .pdb files

From: Grace Brannigan (
Date: Mon Mar 29 2010 - 15:20:39 CDT

Hi Thomas,

If you write to the VMD mailing list, they can recommend the simplest way to
do this in VMD.

If you are just deleting atoms, however, and you like GUIs, I predict that
someone might recommend using the "save coordinates" option under "FILE" in
VMD and then putting in the selection box "NOT index <list of indices of
atoms you want to delete>" and then hitting save. This is just one
possibility for the way you could do the atomselection.


On Mon, Mar 29, 2010 at 12:20 PM, <> wrote:

> Hi Thomas
> I hope you want to edit only PDB file. In that case this might help
> 1] Open your pdb file using "Word Pad" [ keep a copy of original pdb file
> with you]
> 2] Delete unnecessary atom lines
> 3] Save the file [ Do not use "Save As" ]
> 4] Open the file using VMD
> 5] Save the coordinates in pdb format. [ I hope your are familiar with VMD]
> Try this
> Ravi
> > I need to alter some residues by deleting atoms to convert a
> non-standard
> > nucleotide (which I do not have topology information for) into a
> standard
> > nucleotide. The effects of such a change are not important for my
> experiment. I have tried to delete the necessary lines from the pdb and
> then use excel to renumber the atom number column so that all atom
> numbers
> > maintain their original order and are consecutive, however after making
> these edits, VMD can not load the file. I'd appreciate any help with
> this
> > problem.
> > Thanks,
> > Thomas Kahn

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