This is awesome. It looks like this has been a valid setting for a *long*
time, but I've never seen it. I look at a lot of MCSS-type structures,
and I have some really painful scripts that get the bonds right once the
structure is loaded in PyMOL. Now, I can just stamp the CONECT records at
the end of the file and load things up in connect_mode=1 world and
everything works. Speaking of which, I made a little bash shell script to
launch PyMOL this way:
pymol -d "cmd.set('connect_mode',1)" $@
It took me a couple of tries to get that right. The documentation for
command-line options says
-d <string> Run pymol command string upon startup.
so I first tried
pymol -d "set connect_mode,1" $@
but that doesn't work. Is this a documentation typo? I thought a PyMOL
command string was anything you could type at the PyMOL command prompt.
-michael
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it's a cheer-ocracy. | - against HTML email X | Biophysics
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On Thu, 17 Nov 2005, Warren DeLano wrote:
I'm not sure how version-dependent this is, but setting connect_mode to 1
before loading the PDB should disable distance-based connectivity determination.
set connect_mode, 1
load CONECT_only_pdb.pdb
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Eric Zollars
Sent: Thursday, November 17, 2005 5:36 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] displaying protein with propeptide
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
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-----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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