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 origin
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 Tue, 20 Aug 2002, Peter C. McCluskey wrote:
> >The other thing I'd find useful is some molecular mechanics tools,
> >particularly energy minimization. Blending PyMOL with MMTK seems like a
> >good way to do this, since MMTK's license looks fairly liberal.
I think we're all of the same mind on
dee...@iastate.edu (dee...@iastate.edu) writes:
>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 port
> The best way to avoid "derivative work" concern is to code in a "clean room"
> fashion, without reference to someone else's code. In principle, this could
> be done working from the original paper(s) that describe an algorithm.
I assume this is what authors of other packages have done in the pa
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
> licen
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
command available.
The s
> 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 thi
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, th
> 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
Le Sun, 28 July 2002, Nathaniel Echols a écrit
> 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 h
Le Sun, 28 July 2002, Nathaniel Echols a écrit
> 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 h
> 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 t
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
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