Hi,everyone,
Does anyone here could recommend such a database for me? I've searched
the web and only find tools like 'consurf'. Databases like 'consurf' are
important for the analysis of the current known structures. However, for
the original discoveries of new domains, sequence databases with s
Dear all,
Is there any program that can view the fragment files generated from
Rosetta Fragment library?
For example, I want to build a model myself, and I know the secondary
structure of the target protein, so I will dock the 9-fragment myself.
But, at the first step, I have to choose one fragm
Also, there is one more information I forgot to mention---I also have the
NMR assignment(HNCACB spectrum) of the protein, is it possible to combine
the NMR data in my refinement?
Regards,
On Fri, Jan 6, 2012 at 4:14 PM, 商元 wrote:
> Dear All,
>I have a set of 3.2A data containing onl
Dear All,
I have a set of 3.2A data containing only 3000 reflections. From the SAD
phasing and iterative modeling and density modification, I get a
preliminary structure with bad geometric conformations(~8/160 ramachandran
outliers in Coot). After Phenix MLHL refinement, the geometry is still ba
-- Forwarded message --
From: 商元
Date: Wed, Dec 7, 2011 at 6:41 PM
Subject: Re: [ccp4bb] Did anyone here know how to config a local protein
secondary structure prediction server?
To: Jose Duarte
Dear Jose,
Thanks for you kind replies and they are very helpful.
Both HSSP
Hi, everyone,
I want to run plenty secondary structure prediction works and online
prediction costs a lot of time. So I expect local software for secondary
structure prediction will greatly help to my work.
Has anyone ever configed such local secondary structure prediction server?
Any suggestio
Dear members,
I use stereo-view to show my structure, and label the residue name on the
figs. But after labeling, the label and the residues are not in the same
place from the stereo angle. Anyone know how to fix this?
Regards,
Yuan
Hi, everyone,
I can get my protein complex but there are some non-specific aggregation
from the NMR spectra, and chaps can improve it.
So, besides chaps, is there any other detergents to be used during crystal
screening? All suggestions are welcome.
Thanks&Regards,
Yuan
ver it doesn't suffer from the well-known
> singularities as Eulerian & polar angles (it suffers from different
> singularities but it's possible to "sweep them under the carpet").
> Quaternions, as you say, require 4 variables but a constraint is
> needed (i.e. n
Dear CCP4 members,
I have finally used Eleanor's idea, and it works very well. After
applying SSM, we can get a rotation matrix(M), and a displacement vector N:
(Xnew,Ynew,Znew)'=M*(X,Y,Z)'+N
Then, from the rotation matrix M, we can get its another representative
format-*quaternion num
Dear all,
I want to compare the conformational change of two similar structures,
using one alpha helix as the reference. Then, how can I get a vector that
can represent both the position and direction of the helix? Is there any
well-known software can do this？
Or, should I build a cylinder mo
Hello, everyone,
I've a protein sequence of known domain. Based on structure alignment,
I've got a alignment of those with known structures. Then how to add my
sequence to the alignment?Any suggestions?
Regards,
Yuan SHANG
I've seen a website where there are some dynamic pictures to show the
effects of the absence of various diffraction data to the electronic
density, such as the changing process of the electron density as the
deletion of low-resolution data. But I can't find this website now, could
anyone here also
Hi all,
A non-ccp4 question. I found a buried helix in my structure contains
several highly conserved polar residues (as well as some hydrophobic
residues) whose sidechains form extensively interhelical H-bonds with
backbone atoms. I searched in pubmed try to find out some similar
cases but failed
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