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
>
--=20
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand =20
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea +64 3 4797293=20
Fax / Waeawhakaahua +64 3 4797034
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