Re: [PyMOL] displaying protein with propeptide

[Joel T. <joe...@ot...>]

Hi Ann,

I would change the chain id of the propeptide in a text editor, to say P =

and remove the P from after the residue numbers.

J

Anne M=F8lgaard wrote:

>Hi,
>
>I am having problems displaying proteins with unusual residue numbering,=

>such as proteins with propeptides. An example is 1cs8, which 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 =20
>.
>.
>.
>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 =20
>Etc.=20
>
>If I open 1cs8 with PyMol, I can see everything in the "lines", "sticks"=
 and
>"surface" representation, but in ribbon or cartoon mode only part of the=

>protein is shown. What do I have to do to show the whole sequence?
>
>How do I select residues with a "P" appended to the residue number? If I=
 say
>"select resi 1P-5P" I get both 1P-5P and 1-5.=20
>
>Any help will be appreciated! (I am using PyMol version 0.98 for Windows=
).
>
>- Anne=20
>
>--------------------------------------------
>Anne M=F8lgaard, Ph.D.
>Center for Biological Sequence Analysis
>BioCentrum-DTU, Building 208
>DK-2800 Lyngby
>
>Email:  an...@cb...=20
>Phone:  (+45)4525 2472
>--------------------------------------------=20
>
>
>
>
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>

--=20
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                    =20

Pukenga
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Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

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