RE: [PyMOL] displaying protein with propeptide

[Warren D. <wa...@de...>]

A quick fix is to use the "retain_order" setting.

set retain_order

which will force PyMOL to honor the order of ATOMs in the PDB file over =
the numeric ordering of residue identifiers.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Joel Tyndall
> Sent: Thursday, November 17, 2005 12:15 PM
> To: Anne M=F8lgaard; pym...@li...
> Subject: Re: [PyMOL] displaying protein with propeptide
>=20
> Hi Ann,
>=20
> I would change the chain id of the propeptide in a text=20
> editor, to say P and remove the P from after the residue numbers.
>=20
> J
>=20
> Anne M=F8lgaard wrote:
>=20
> >Hi,
> >
> >I am having problems displaying proteins with unusual residue=20
> >numbering, such as proteins with propeptides. An example is=20
> 1cs8, which=20
> >starts off like
> >this:
> >
> >ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> >N =20
> >ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> >C =20
> >ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> >C =20
> >ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> >O =20
> >ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> >C =20
> >ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> >O
> >.
> >.
> >.
> >And later on comes the sequence corresponding to the mature protein:
> >
> >ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> >N =20
> >ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> >C =20
> >ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> >C =20
> >ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> >O =20
> >ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> >C
> >Etc.=20
> >
> >If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> >"sticks" and "surface" representation, but in ribbon or cartoon mode=20
> >only part of the protein is shown. What do I have to do to=20
> show the whole sequence?
> >
> >How do I select residues with a "P" appended to the residue=20
> number? If=20
> >I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> >
> >Any help will be appreciated! (I am using PyMol version 0.98=20
> for Windows).
> >
> >- Anne
> >
> >--------------------------------------------
> >Anne M=F8lgaard, Ph.D.
> >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20
> >DK-2800 Lyngby
> >
> >Email:  an...@cb...
> >Phone:  (+45)4525 2472
> >--------------------------------------------
> >
> >
> >
> >
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> >
>=20
> --=20
> Joel Tyndall, PhD
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> Lecturer
> National School of Pharmacy
> University of Otago
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