mple code that would read
a PDB and mtz and calculate real space fit for an aminoacid, or generating
symmetry neighbours from a asymmetrical unit PDB and its space group. How
are people doing things like that in 2024?
Cheers,
Lucas Bleicher
I've been compiling a reference database and I've just noticed that it's quite
difficult to automatically retrieve references for most articles on
crystallographic software. Has anyone noticed that? It seems that, for some
reasons, articles on the "Computer programs" section on Journal of Applie
By the way, is there a program (perhaps one of those cited on this thread) that
would list all salt bridges and hydrogen bonds for residues in the same chain?
Lucas
Veja quais são os assuntos do momento no Yahoo! +Buscados
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Some time ago I've heard about the idea of proposing
an ensemble of models (as in NMR), instead of a single
model for x-ray crystallography structures. If I
remember correctly, this idea has been published
somewhere. Can anyone tell me what article is that?
Lucas
Abra sua conta no Yahoo! M
I've had a very good experience with MrBump:
http://www.ccp4.ac.uk/MrBUMP/
Not only because of the program itself, which was able
to find an unexpected template for the problematic
chain (the first one was straightforward in Phaser),
but also because of great support from Martyn & Ron.
It's defin
That would be a great idea. In fact, I keep on my
mailbox dozens of great postings (most of them
summaries) in CCP4 which would be very useful to
everybody if there's an online resource, with
information organized in topics. I would gladly copy
them to this wiki.
Lucas
--- Kay Diederichs <[EMAIL
tp://www.esrf.eu/computing/scientific/FIT2D/
See also:
http://www.datasqueezesoftware.com/
For source code try:
http://cctbx.sourceforge.net/current_cvs/python/iotbx.detectors.html
Good luck,
Jon
==
Thanks a lot,
Lucas Bleicher
Novo Yahoo! Cadê? - Experimente uma nova busca.
http://yahoo.com.br/oqueeuganhocomisso
could study?
Thanks,
Lucas Bleicher
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By the way, I'll extend that question: the validation
software Verify3D assigns not only buried state but
also polar fraction and secondary structure, using the
probability of finding given residues in the different
"environment" defined when combining all this
information to calculate a "score" of
--- Juergen Bosch <[EMAIL PROTECTED]> escreveu:
> How about Coot ? Click the residue you want to
> change and hit Resdiue
> Property.
That's how I used to do it, but things start to become
boring when one needs to do it with more than one pdb
file with about 200 residues each. Does coot accept
so
Is there a program in CCP4 with a command to change
the B-factor of a single residue? I checked the
documentation for pdbset and it seems to assign
B-factors only for the whole molecule.
What I'd like to do is plot a given residue property
in a graphic software using the "color by b-factor"
featur
I remember reading once or twice people requiring
examples of PDBs which contained ordered His-tags.
Someone did a survey on this, which is on the latest
Acta Cristallographica D:
http://journals.iucr.org/d/issues/2007/03/00/en5203/index.html
Lucas
___
--- Marius Schmidt <[EMAIL PROTECTED]>
escreveu:
> Dear colleagues,
> I was wondering whether someone of you has
> reported/published
> new or improved crystallographic software somewhere
> else than Acta Cryst. It would be nice if you could
> share your experience with me. Topics might be:
> - qu
When I was checking a structure and preparing figures
for an upcoming article, I found out that Procheck and
Pymol use different criteria to assign secondary
structure for residues in a PDB (i.e.: some residues
that appeared as loops in the cartoon representation
in pymol were assigned as beta-stra
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