Is there a similar command to force PyMOL to use only CONECT lines in
the pdb file instead of generating connectivity by distance?
Eric
Warren DeLano wrote:
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.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
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-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Joel Tyndall
Sent: Thursday, November 17, 2005 12:15 PM
To: Anne Mølgaard; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] displaying protein with propeptide
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 Mølgaard 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
ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08
C
ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91
C
ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82
O
ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28
C
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
ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80
C
ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33
C
ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43
O
ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50
C
Etc.
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.
Any help will be appreciated! (I am using PyMol version 0.98
for Windows).
- Anne
--------------------------------------------
Anne Mølgaard, Ph.D.
Center for Biological Sequence Analysis BioCentrum-DTU, Building 208
DK-2800 Lyngby
Email: a...@cbs.dtu.dk
Phone: (+45)4525 2472
--------------------------------------------
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--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
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