Hello,
We plan to use PyMOL as the alignment/structure viewer in a protein
threading package we developed. Mostly there will be some new
features/enhancements on the existing viewer. e.g.
- highlight/color by mappings of amino acid porperties (cysteines, charge
and hydrophobicity, size, secondary
Hello,
I'm wondering if it's possible to simulate RasMol-styled "strand"
representation (a number of smooth curves that run parallel to one another
along the peptide plane of each residue). I would like something like that to
repersent gaps in a structural alignment (i.e. a segment that doesn't "e
Hello,
I was following instructions in setup/INSTALL.win32 (as in pymol-0_90-src.tgz)
to build PyMOL. I have all the external components (glut, zlib, libpng) in
place. When I tried
python setup.py build
It generated linker errors:
C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL
Hello,
Eh, I think this is a rather basic question. So I built PyMOL on Win32, tried
to run pymol.bat, which calls python $PYMOL_PATH/modules/pymol/__init__.py,
which complained:
Traceback (most recent call last):
File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py", line 92, in ?
don't understand why it
doesn't import that. Anyways, it seems to be up. I guess every time I build
PyMOL, I'll have to copy the _cmd.pyd file over.
Tina
- Original Message -----
| From: "Tina Li"
| To:
| Date: Mon, 25 Aug 2003 11:57:27 -0400
| Subject: [PyMOL] cannot find _c
50)-346-1154
| Fax (650)-593-4020
|
| > -Original Message-
| > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
| > ad...@lists.sourceforge.net] On Behalf Of Tina Li
| > Sent: Wednesday, August 27, 2003 8:34 AM
| > To: pymol-users@lists.sourceforge.ne
Hello,
I'm trying to add another external GUI to be positioned at the bottom of the
structure window for displaying sequence alignments, with not much luck. Here
is what I want and what I've done:
Goal: when opening a sequence alignment file in the existing GUI, launch a new
GUI at the bottom dis
Hello,
Is there an alternative loading PDB coordinates, other than "load "?
Let's say after threading against a large database of protein templates, I
need one PyMOL script generated for each of the templates. I could as well
generate one PDB file for each to load, but it would be difficult to man
Warren,
That's exactly what I need for cutting down on the number of unnecessary
files! Thank you!
(...wondering how many hidden goodies are out there...)
Tina =)
- Original Message -
From: "Warren L. DeLano"
To: "'Tina Li'" ;
Sent: Tuesday, Sep
Hello,
I have two operations that I want to perform, and am not aware of a simple way
(if possible) of doing them. So here it goes:
1. how (if possible) to retrieve the color for a residue as identified in an
expression, e.g. "resi 9"? Note that it's not a range so no multiple answers
is possible
Hello,
I have two questions:
1. I want to superpose object1 and object2 on top of each other, and have
derived a rotation matrix to transform object2 by. How do I apply this matrix
to all its atoms? Either I parse its PDB coordinates, multiply them by the
matrix, and load the object (which can be
Hello,
I wonder if there is a quick and simple way of detecting whether a selection
exists without triggering any errors. e.g. to check if there are currently any
atoms picked (and collect the residue IDs if there is any), I do:
cmd.iterate("(lb)","stored.list.append((resi))")
if no atoms were p
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