@all,
we've been comparing various programs during our SGPP times (that was
about 2 years ago) Sharp, Shelx, bp3, mlphare, SnB (BnP). If I
remember it correctly at that time Sharp was the winner, although the
site finding was the major bottleneck/problem. What we ended doing was
finding sites (SeMet) by an external program (most of the time Shelx)
and feeding them into Sharp.
I do remember long time ago the setup on a G5 MacPro which worked
fine, I did have quite some exchange with Clemens to get it running
though - mostly because I'm a user and not a programmer.
On a side note we also looked at HKL, Mosflm, XDS processing of data,
we observed differences in the ability of e.g. Shelx to locate SeMet
sites depending on the processing program you used. Of course perfect
data was undistinguishable, but some datasets which were more tricky
to process showed significant differences in locating the SeMet
positions. In those cases XDS was better. This is of course running
all programs with their default parameters and not tweaking them.
Jürgen
On 27 Oct 2008, at 08:30, Clemens Vonrhein wrote:
Dear Pete,
just my personal view on this (so don't take this as a legal expertise
regarding our SHARP licence). I don't have any problems with people
comparing software programs - I do that all the time. I doubt this can
be seen as reverse engineering.
The tricky part comes when comparisons are being published: ideally it
would be nice if every developer of a particular piece of software is
given the chance to comment - maybe he/she could even give a few
simple advices how to run the program. After all, different programs
might have different set of defaults (conservative versus
adventurous) for particular problems.
It's similar to a problem we discover e.g. in a PDB entry: contacting
the authors of that PDB entry first to give them a chance to comment
(and correct) I think is the apropriate initial step. Or actually -
lets rephrase that: it's not like an error in a PDB entry!
Improvements in software benefit a lot more crystallographers whereas
a fixed PDB entry usually concerns a much smaller group of us.
Anyway, I think we're doing actually fairly well compared to other
scientific fields: crystallographic method developers are a very
friendly bunch I must say, even if we're in a kind of 'competition'.
Cheers
Clemens
On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote:
Apologies for going slightly further off-topic...
Last time I had a free half-day to look into sharp, I noticed that
the
academic license prohibits reverse-engineering. This seemed to put
any
comparative testing into a slightly grey area. For example, if I
find
that sharp does the best job refining sites, but bp3 outputs better
phases for a dataset due to different representation of phase
probabilities*, I've implicitly constructed a primitive model of how
sharp is working. This seems close enough to a first step of
reverse-engineering that I was concerned.
Could someone confirm that I'm worrying about things I don't need
to here?
Pete
* Purely hypothetical example.
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Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
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