Dear Jeff,
I have an utility which can apply any operator, specified by the user as
e.g. -y,x+1/2,z-2/3 etc. You could use it to build your "crystal". Your
molecule should of course have the right starting position and you have
to figure out the correct operators yourself. If you are interested, I
Dear Chen
You are subscribed to the CCP4BB group as [1]chenc...@gmail.com in fact, so
you may have registered your password with a different form of your address.
To rectify this, please make sure you are logged out of JISCMail, then go to
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Dear colleages,
Currently I met problem in a MR case and hope somebody could advise me.
The crystals belong to sg C2221 with the cell parameters a=59A, b=302A,
c=97A, beta=92.3. The searching model shares 43% identities (300aa) with
target protein. When searching in PHASER program, only o
Hi,
Those are very high scores, which usually mean that the solution is correct.
One thing I'm wondering about -- when you run xtriage, does it report that you
have translational non-crystallographic symmetry? Pseudo-translations can
cause problems in molecular replacement.
Other than that, I
Hi,
How sure are you of the space group ? What are the data processing Rsym values
(which if high may indicate mis-indexing due to an incorrect choice of detector
origin for
example) ? There are many places where things can go "wrong" before reaching
the molecular replacement calculation stage
Perhaps Section 7.9.1 might be of some use?
http://lmb.bioch.ox.ac.uk/coot/doc/coot/Validation-Graphs.html#Validation-Graphs
Cheers,
Paul.
On 28/11/10 06:14, Albert Guskov wrote:
I noticed the same problem on Mac OSX (snow leopard) . Seems to be an
issue for all phenix installation packages f
On 11/29/10 08:16, xiuwen zhang wrote:
Dear colleages,
Currently I met problem in a MR case and hope somebody could
advise me.
... Moreover, as suggested by matthews_coff, there should be at
least 2 molecules in one ASU
Making what assumptions about acceptable values for matthews_
Dear All
Currently I'm refining my model in refmac5, so is there a way I can switch to
phenix.refine by retaining the same R-frees, I have from refmac? Any
suggestions at this time would be helpful!
Thanks in advance!
Thanks!
Jyotica
I can't see any problem switching from Refmac to Phenix refinement. You just
provide Phenix with the current model (if you have refined using TLS there is
an "additional"
step, using I believe tlsanl to generate the "proper" PDB file as you would for
data deposition with the pdb), the initial m
On Mon, Nov 29, 2010 at 02:44:01PM +, Frederic VELLIEUX wrote:
> I can't see any problem switching from Refmac to Phenix refinement. You just
> provide Phenix with the current model (if you have refined using TLS there is
> an "additional"
> step, using I believe tlsanl to generate the "prop
Hi all,
I read/heard that hydroxyapatite column can be used to purify proteins, getting
separation results orthogonal to ion exchange and size exclusion chromatography.
I was wondering if any of you would be kind enough to share her/his experience
with me, and would suggest vendors and models for
On Mon, Nov 29, 2010 at 6:50 AM, Tim Gruene wrote:
> But you have to make sure that refmac5 uses the same integer for flagged
> reflections as refmac does. If I remember correctly, the default in the
> ccp4i
> gui for refmac is 0 or 1 (out of usually 0-19 for 5% of flagged
> relfections),
> but I
On Mon, 2010-11-29 at 14:30 +, Jyotica Batra wrote:
> is there
a way I can switch to phenix.refine by retaining the same
>
R-frees, I have from refmac
If you actually mean the test set,
then you don't need to do anything
other than use the same
mtz-file. Keep in mind though that in phenix b
I was wondering if any of you would be kind enough to share her/his
experience with me, and would suggest vendors and models for such columns.
I really like "ceramic" hydroxyapatite from Bio-Rad. The only type that
behaves in the columns long-term, without the need for repacking. It also
gives
Dear Xiuwen,
First, I cant see how the space group is C2221 with a beta of 92.3
Maybe you need to clear the symmetry confusion before getting
additional pseudo-symmetry suggestions.
A.
On Nov 29, 2010, at 14:16, xiuwen zhang wrote:
Dear colleages,
Currently I met problem in a MR ca
Dear Colleagues,
We are pleased to announce that registration is now open for the International
Conference on Structural Genomics 2011, which will be held in Toronto, Canada
on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings
of the International Structural Genomics
Hi Sebastiano,
Just to add to Dima's response, I've used ceramic hydroxyapatite column and
got great results separating 2 very large membrane proteins complexes that
eluted together in DEAE/Q and ran in similar size range in SEC. One eluted
in 100-200mM KPi and the the other in 300mM+ KPi ~pH 7.4.
I have arachidonic acid soaked into my crystal structure and want to model it.
The phenix.refine is allowing my cis double bonds to distort to a gauche or
trans form. Is it the cif file or the refinement restraints in the program that
I need to correct.
Are you sure that the mtz file you are refining against has spacegroup
C2221 in the header? Phaser can test C222 and C2221 but when you start
refinement you need to be sure the data header is correct.
Another possible bug - is the model elongated in any way - they
sometimes need surface loops
On 29/11/10 16:17, Nathaniel C. Gilbert wrote:
I have arachidonic acid soaked into my crystal structure and want to model it.
The phenix.refine is allowing my cis double bonds to distort to a gauche or
trans form. Is it the cif file or the refinement restraints in the program that
I need to co
Dear Chen,
It looks like you have a unit cell with two relatively short axes and one long
one - and some disorder. I have experienced a few examples of this with virus
fibre proteins (adenovirus fibre and T4 short tail fibre). For the short tail
fibre we also obtained images in which some line
Hi
The absence of clearly separate lunes on the first image indicates that the
mosaic spread is rather high. If you increase the intensity threshold in spot
finding you may be able to pick out spots belonging to a single lattice. If you
increase the intensity threshold in autoindexing you may a
Nathaniel
I made a small mod to eLBOW (which will be available in the next
nightly build) that allows you to get an all cis ACD from a SMILES
string. I have attached the result. Note that the name of the file has
for the four cis (zusammen) configurations. As Paul suggested,
the torsion value
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