sometimes change in ph also dissocaites the complex,so you need to screen
best buffer ph for your protein complex.
atul kumar
On Sun, May 23, 2010 at 8:18 PM, Maia Cherney wrote:
> Original Message
> Subject:Is it possible for the Tris buffer to strip the Zn ions
> fro
Hi crytallographers !
I am attempting to use the Low Ionic Strength Screen™ from Hampton Research.
I realised that the kit recommended a 4ul Sample to 7ul screen drop.
Has anyone reduced this amount for hanging drop? for example 1ul sample to
1ul screen ? or 1ul sample to 1.75ul screen?
Any hel
unambiguous space group ?
Jürgen
On May 23, 2010, at 4:52 PM, Paul Lindblom wrote:
> Thank you all for your quick answers. I already tried the phyre server but
> could not find a appropriate model. Balbes found a structure with 29%
> identity, but no solution. Now I am running molrep with the
> Phyre is a fold-recognition server...
And one might argue that "recognising the fold", getting the
loops/boundaries in the right place is the first step towards getting
MR to work properly - which is what I think Phyre does rather well.
But I absolutely agree that an approach like this requires
Thank you all for your quick answers. I already tried the phyre server but
could not find a appropriate model. Balbes found a structure with 29%
identity, but no solution. Now I am running molrep with the model balbes
found...
2010/5/23 Nathaniel Echols
> On Sun, May 23, 2010 at 12:57 PM, David
On Sun, May 23, 2010 at 12:57 PM, David Briggs wrote:
> I like to generate some models using the "Phyre" server
>
> ( http://www.sbg.bio.ic.ac.uk/~phyre/ )
>
> Feed the best .pdbs into Mr Bump.
>
> Go and get coffee. Come back and find a solution with post-refmac
> R/Rfree in the mid-30s.
>
> IMHO
Try balbes. It needs only your sequence and your mtz file.
http://www.ysbl.york.ac.uk/~fei/balbes/
Maia
Paul Lindblom wrote:
Hi everybody,
I just crystallized a new project protein. How can I find a possible
model for using molecular replacement? I have the sequence of my
protein. Is it e
I'll add another molecular replacement anecdote to the growing list:
I like to generate some models using the "Phyre" server
( http://www.sbg.bio.ic.ac.uk/~phyre/ )
Feed the best .pdbs into Mr Bump.
Go and get coffee. Come back and find a solution with post-refmac
R/Rfree in the mid-30s.
IMHO,
I recently used an ensemble of many proteins with Phaser. A single model did
not find a solution but this ensemble of seven very similar molecules gave a
correct solution with a TFZ of ~9.0. I did not trim the side chains in this
ensemble (first try worked) but this introduced variation may be b
XtalPred
http://ffas.burnham.org/XtalPred-cgi/xtal.pl
or if you have data already let Balbes do the job.
Jürgen
On May 23, 2010, at 3:34 PM, Miri Hirshberg wrote:
> Sun., May 23rd 2010
> EBI
>
> Paul,
>
> 1. yes you can run your sequence against all PDB.
>
> 1. http://www.ebi.ac.uk/pdbe-srv/
Sun., May 23rd 2010
EBI
Paul,
1. yes you can run your sequence against all PDB.
1. http://www.ebi.ac.uk/pdbe-srv/view/
drop the one letter sequence in the sequence box
and search
2. http://www.ebi.ac.uk/Tools/fasta33/index.html
From the Databases protein you pick
Protein structure Sequence
Hi everybody,
I just crystallized a new project protein. How can I find a possible model
for using molecular replacement? I have the sequence of my protein. Is it
enough to make a sequence search in the pdb? Or is there another approach I
can use?
Thanks a lot,
Paul
Hi Ian,
On 5/23/10 5:01 AM, Ian Tickle wrote:
Thanks a lot! Actually my map has very weak density at only certain
region, and I want to numerically say that this region is "weakly"
correlated to the atomic map at this region. But according to the CC
formula, if investigating by residue, CC only
Original Message
Subject: Is it possible for the Tris buffer to strip the Zn ions from
the Zinc Finger motif of a protein?
Date: Sun, 23 May 2010 08:45:55 -0600
From: Maia Cherney
To: ruheng
The complex can dissociate without loosing Zn. For example, if you
dilut
>I’m trying to prepare an alignment figure of 2 proteins that highlight
>conserved and similar residues and probably secondary structures; I will
>greatly >appreciate it if anybody can recommend a software that I can use.
>Thanks, Mohd
For those who like TeX, TeXshade is incredibly powerful, an
On Sun, May 23, 2010 at 5:24 AM, Pavel Afonine wrote:
> Hi,
>
>
> On 5/22/10 8:23 PM, Zhang, Hailiang wrote:
>>
>> Thanks a lot! Actually my map has very weak density at only certain
>> region, and I want to numerically say that this region is "weakly"
>> correlated to the atomic map at this regio
Hi Mohd
You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment
Editor for Publication Quality Figures)
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
It's quite nice and has a lot of potential, although unfortunately it seems
that development of the software as
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