Hello All,
I am a long-time Molscript user and devotee and am trying to make the
move to PyMol for various reasons. A lot of the structures I work with are
at moderate-low resolution making automated secondary-structure prediction
difficult and most of them don't contain SS flags in the
I've got a crude interface to the RasMol code which lets you run RasMol's
secondary structure assignment code from PyMOL at:
http://www.rahul.net/pcm/rasmolapi.tar.gz
I don't make any promises as to how well it works or whether I will ever
get around to cleaning up the ugly code.
If there are
On Mon, Jul 29, 2002 at 01:12:40PM -0400, Nathaniel Echols wrote:
How hard would it be to incorporate the DSSP algorithm? I was looking at
the source for RasMol, which has a complete implementation. My feeling is
that this could be ported without too much misery. However, RasMol's
license
Le Sun, 28 July 2002, Nathaniel Echols a écrit
snip
but I'm working on making it more general. I suppose since I only use
this for loading files into PyMOL, I could just write it in Python as a
PyMOL module. . . would that be useful to anyone else?
Yes, please. There are some structures that
Le Sun, 28 July 2002, Nathaniel Echols a écrit
snip
but I'm working on making it more general. I suppose since I only use
this for loading files into PyMOL, I could just write it in Python as a
PyMOL module. . . would that be useful to anyone else?
Yes, please. There are some structures that
Yes, please. There are some structures that have to be generated by using
symmetry operations defined in the REMARK 350 lines in the pdb file
(example:
1jjy.pdb). The only way (I know of, if you know a better one, please tell me)
to
do this is going to http://pqs.ebi.ac.uk where the
Nat,
You read my mind. Having just converted the output of DSSP manually to PDB
records last week I was eyeing the source to util.ss wondering how to turn it
into a dssp parser.
Ideally util.ss could become a shell that would know (from the environment?)
if dssp or similar was installed,
Ideally util.ss could become a shell that would know (from the environment?)
if dssp or similar was installed, then either run dssp and parse the output
to assign the ss, or else run the ss asignment code in the current util.ss if
no other options were available.
I've basically done this,
OK, heres what we've got:
The DSSP program is available for Linux and Windows from
http://www.cmbi.kun.nl/swift/dssp/ .
I have written a Python script that parses the output of DSSP and alters
the annotation in PyMOL. You just start the script, then You have a
dssp object
command available.
Dear Pymol users,
I am very pleased with Pymol as a visualization tool for the generation of
publication quality images, but I am having a problem with one aspect of the
problem. I am working with several PDB files that do not have embedded
secondary structure assignments. I have been trying to
programs. So I am in search of a solution. Can one manually create a
secondary structure assignment matrix to insert into the PDB file? I must
admit that as a novice I do not understand the formatting of the secondary
structure matrices that I have seen embedded in some PDB files. Is
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