[Biopython] writing a PDB----PLEASEEEE HELP

[Eric Talevich]

Hi Martin,

It sounds like VMD displays just one model at a time, unless you make a
movie out of it. You could get around that by writing the two structures as
two different chains within the same model.

But if the goal is just to view two structures superimposed, you'd be better
off scripting your molecular viewer of choice to do it for you.

In PyMOL, to view 1ABC and 2XYZ (made up), write this to a file called
1ABC_vs_2XYZ.pml:

# This is a generated PyMOL script
load /path/to/1ABC.pdb, 1ABC
load /path/to/2XYZ.pdb, 2XYZ
align 1ABC, 2XYZ

# Optional viewing tweaks
hide all
show cartoon, 1ABC
show cartoon, 2XYZ
reset


Then launch the viewer from the command line:
pymol 1ABC_vs_2XYZ.pml

If the two structures don't have the same peptide sequence, you'll have
better results with the "fit" function instead of "align":
http://www.pymolwiki.org/index.php/Fit

I know VMD has something similar, but I don't have an example offhand.

Best,
Eric


On Tue, Oct 26, 2010 at 1:05 PM, martin djokovic
<martin.djokovic at gmail.com>wrote:

> Hello David and everyone else,
>
> Yes David at the moment I am actually doing that-formatting the PDB into 2
> models then superimposing them.
> Merging the structures when they are in 2 differant PDB files is not
> working.
> I tried the following:
> from Bio.PDB.Model import Model
> model1=Model(2ndModel)
> structure1.add(model1)
> Its not working-I think I might have to better understand the object
> "structure"
> Is there a better way to merge two structures? Else I will write the 2 pdb
> files as models into a single PDB then superimpose.
>
> Another question-maybe some of you use VMD-if I open 1JOY in VMD I can only
> see one of the models, I need to scroll using the scroll bar to see the
> others-I cannot see them all at once.
> So for running the warwick code and seeing its eefect I use RASMOL, is
> there
> a way to look at all the models in the same time without scrolling in VMD?
> I
> prefer VMD to RASMOL so just wondering about that.
>
> Thanks everyone foe all the help.
>
>
> On Mon, Oct 25, 2010 at 11:49 AM, Lapointe, David <
> David.Lapointe at umassmed.edu> wrote:
>
> > Hi Martin,
> >
> > If you  look at the PDB structure files based on NMR determinations,
> you'll
> > see that they contain different models. Perhaps you can format the file
> that
> > way. For example look at 2GDT.pdb
> >
> > David
> >
> > -----Original Message-----
> > From: biopython-bounces at lists.open-bio.org [mailto:
> > biopython-bounces at lists.open-bio.org] On Behalf Of Peter Cock
> > Sent: Monday, October 25, 2010 11:33 AM
> > To: martin djokovic
> > Cc: biopython at lists.open-bio.org
> > Subject: Re: [Biopython] writing a PDB----PLEASEEEE HELP
> >
> > On Mon, Oct 25, 2010 at 4:26 PM, martin djokovic
> > <martin.djokovic at gmail.com> wrote:
> > > Hi Peter,
> > > I want a new PDB with structures A and B superimposed so that I can see
> > them
> > > both at the same in the same file
> > >
> > > So at the end of the simulation/run  I would have A and B (original)
> and
> > the
> > > 'ans.pdb' with A as it was but B rotated and translated to be
> > superimposed
> > > on A in the same PDB
> > > I want to try this first simple superimposition but actually I want to
> > > connect A and B together to make a longer strand
> > > The last residue of A and first residue of B are the same so I can use
> > those
> > > coordinates to rotate/translate B then connect to A
> > > I can do that manually using SWISS PDB but I want to do it for many
> > > structures and its time consuing.
> >
> > Won't that mean there would be a duplicate residue? i.e. The last residue
> > of A and first residue of B are the same thing, but would be in the file
> > twice.
> >
> > Anyway - that basic idea is you must create a Bio.PDB structure object
> > with both A and B in it (perhaps as two chains in the same model), then
> > write that to the PDB file. The details depend on how you want to do
> > the combination - there is more than one way to represent  A and B
> > in the same PDB file (quite separate from how to do it in Biopython).
> >
> > Peter
> >
> > P.S. You could trying writing out two separate PDB files and try simply
> > concatenating them... it might do what you want.
> >
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