On Wed, Mar 31, 2010 at 8:47 AM, Dirk Kostrewa
wrote:
> this is very interesting! From the list of changes, it appears that in
> version 1.6.1, you use a similar idea to implement hydrogen bonds via DSSP
> during refinement that I used to stabilize the 4.3 A refinement of Pol II in
> complex with
> to my knowledge, none of the existing reciprocal-space refinement
> programs is really suitable for low-resolution refinement. In my
For what it's worth, I've had good luck with refmac5D, which
incorporates an SAS target into model refinement (I believe this was has
now been incorporated into th
Phil Evans wrote:
Does anyone have a good way of imposing secondary structure restraints
in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints within
helices, input to refmac as "LINK"s , with the list generated with a
little program and certain amoun
Dear Phil & CCP4ers,
to my knowledge, none of the existing reciprocal-space refinement
programs is really suitable for low-resolution refinement. In my
opinion, what is clearly missing, are automatic hydrogen-bond-
restraints that would stabilize all secondary structures and other
structur
I put together a simple perl script to take WHATIF optimal hydrogen
bonds from a known structure and generate refmac or cns restraints. You
can limit it to backbone or all h-bonds.
Refmac:
http://hood.icmb.utexas.edu/~paul/ccp4_hbond
CNS:
http://hood.icmb.utexas.edu/~paul/cns_hbond
Phil Evans
Phil,
I have a student who has been working on a python script that will allow
the user to manually define hydrogen bonds in pymol (i.e. click on the
nitrogen and oxygen atoms that you want to restrain). It then outputs a
restraints definition file for refinement in phenix. It can be tedious
I would guess that it would be easier to restrain a helix by hydrogen
bond lengths rather than by phi/psi torsion angles, and that could
work for sheets as well.
Phil
On 8 Jan 2009, at 19:05, Garib Murshudov wrote:
If top/par file could be converted to the following type of
instructions
If top/par file could be converted to the following type of
instructions then you do not need to define everything in cif file
(these are for torsion angles, all other restraints can be defined
similarly)
General torsion angle restraints for any quartet of atoms:
external torsion first cha
Hi Phil,
sorry, haven't read you question properly. No idea how to get easily
from top/par to cif for refmac.
Probably would need a little scripting, but that's been exactly your
question ...
Eckhard
XPLO2D from the USF-Suite does this:
You feed it a PDB file of the model to which you
XPLO2D from the USF-Suite does this:
You feed it a PDB file of the model to which you want to restrain your
refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program gener
Does anyone have a good way of imposing secondary structure restraints
in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints within
helices, input to refmac as "LINK"s , with the list generated with a
little program and certain amount of pain
refm
For a (very) low resolution RNA/protein complex in which we had high(er)
resolution structures for both components, I used the optimal hydrogen
bonds from these structures (WHATIF output) as restraints. I made a
couple perl scripts to take this output and generated either CNS or
REFMAC restrain
lt;[EMAIL PROTECTED]>
>To:
>Subject: [ccp4bb] secondary structure restraints
>
>I am trying to build and refine a model into 3.6 angstrom Se-met phased
>maps. What is the best way to define secondary structure restraints for
>refinement? (hydrogen bonds? backbone torsion angl
I am trying to build and refine a model into 3.6 angstrom Se-met phased
maps. What is the best way to define secondary structure restraints for
refinement? (hydrogen bonds? backbone torsion angles?) Are there any
tools available to help me define restraints for a specified region, or
do I hav
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