The Richardson's have another tool for RNA backbone rebuilding which *may*
help called RNABC - RNA Backbone Correction.
http://kinemage.biochem.duke.edu/software/rnabc.php
On Thu, Apr 16, 2015 at 8:22 AM, Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:
> Dear all,
>
> Despite molprobit
Dialing Pretty,
It is certainly possible to observe real conformations of amino acids,
especially Arg, that are not quite common enough to have been identified as
rotamers. To this point, note that defined rotamers accounted for only 82%
of Arg conformations in the highly validated data set used t
Monica,
I struggled with this a lot too. I had some success with low molecular
weight PEG (100-400) as a solvent, its well worth a try.
-bob
On Wed, Oct 15, 2014 at 9:13 AM, Monica Mittal
wrote:
> Dear All
>
> Can anyone give suggestions for handling the solubility problem of
> highly hydrophob
Hi Jacob,
Lorena Beese has a few systems where snapshots of reaction mechanisms
have been looked at structurally.
Here are two such papers:
Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein
farnesyltransferase at atomic resolution. Nature Oct 10;
419(6907):645-50.
http://www.ncb
Hi Jacob,
This sounds like what you get from ddmp (
http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html ).
Good Luck,
-bob
On Mon, Nov 28, 2011 at 5:22 PM, Jacob Keller
wrote:
> Dear Crystallographers,
>
> is there a ccp4 program--or otherwise--which can compute ca-ca
> distances
Hi Halliang,
If the ligands are in the pdb het dictionary I think MolProbity will
look at bonds and angles...maybe even dihedrals.
Cheers,
-bob
On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang wrote:
> Hi there,
>
> I want to found some bad geometry for my ligand (sugar rings). The
> procheck .ou
Hi Cale,
My advice would be to find someone local with experience in scripting
possibly in python or perl. This is a tractable problem with a bit of
scripting and if you aren't already experienced this may be a good
opportunity to delve into a bit of programing.
Good Luck,
-bob
On Tue, Mar 8, 201
Hi,
I've pasted below the reasons from Dan Gewirth and the HKL2000 manual
authors for having a -3 sigma cutoff... I'll add briefly that if you
assume the weak data has a Gaussian distribution around zero a -3
sigma cutoff allows you to record ~99.8% of the data.
-bob
SIGMA CUTOFF
Cutoff for reje
Hi Jacob and Mike,
An additional thought exercise would be to consider if your
exogenously added protein is itself heritable. Essentially trying
Mike's idea 1, but instead of expecting the protein to get into the
genome and in that way have it's "information" stored, look to see if
the protein it
Tuhin,
I have had some success with low molecular weight PEG eg. PEG200.
-bob
On Thu, May 13, 2010 at 1:00 PM, Tuhin Bhowmick
wrote:
> Dear All,
> does anyone have any clever suggestion/s for handling the solubility problem
> of highly hydrophobic compound, during co-crystallization or inhibiti
Kelly,
This can be done with the Swiss-PDBviewer itself.
Download the viewer if you don't have it.
load your pdb ( File > Open PDB File... )
load the sequence you want to thread (fasta format) ( SwissModel >
Load Raw Sequence from Amino Acids...)
then thread with ( Fit > Fit Raw Sequence)
Good L
Hi John,
Another way to get at this data is to run your structure through
MolProbity (http://molprobity.biochem.duke.edu/). After this on the
mainpage there in the downloads section...if you go to *all
downloads*... there is a raw_data section that contains the
ramachandran stats (PDBid-rama.data
Roberto,
An also less than optimal work around might be to take your refined
.pdb from PHENIX or CCP4 and run it through the downgrade utility on
MolProbity to change to PDBv2.3 format before working in Coot. I
don't think it is necessary to convert back to PDBv3.0 for
phenix.refine, but MolProbi
CCP4ers,
We have recently become interested in the use of TLS parameters for
studying protein dynamics. In particular, we would like to generate
an ensemble of conformations along the TLS trajectories to use as a
starting point for protein design. Before jumping into this though,
I'd like to ask
Xiaoyi,
When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.
http://molprobity.biochem.duke.edu/
It is a bit of a process, but here's the rundown:
Load your .pdb into molprobity
Add hydrogens
Visualize interface contacts
Then sele
Hi Xiaofei,
You might want to try the backrub tool in KiNG
(http://kinemage.biochem.duke.edu/software/king.php) .
This allows one to make subtle correlated changed along the mainchain,
and watch the effect on the fit to the Ramachandran plot.
Richardson Lab
Duke University
On 8/3/07, Xiaofei J
For dealing wih PDBv3.0 format, our lab has two new facilities to
offer:
MolProbity, our structure validation and improvement webserver
(http://molprobity.biochem.duke.edu/ ), now accepts coordinate files
in
either PDBv2.3 or PDBv3.0 format and uses the latter for computations.
A formal descri
uoted text -
On Tue, 8 May 2007 19:41:13 -0400
"Robert Immormino" <[EMAIL PROTECTED]> wrote:
Forwarded Conversation
Subject: [ccp4bb] Program to evaluate RNA torsion angles?
From: Yuan Lin <[EMAIL PROTECTED]>
Reply-To: Yuan Lin <[EMAIL PROTECT
Molprobity has a great tool for this under the section Visualize
interface contacts. One caveat though, if the small molecule isn't
already in ligand depot you have to provide your own PDB format
description.
On 2/27/07, mathias <[EMAIL PROTECTED]> wrote:
Dear all,
Can anyone of you guys reco
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