Hi all,
I work on a protein that has two know space groups at the same
condition. One is P21 with 1 molecule in the ASU (small cell) and
the other is P21 with 2 molecules in the ASU (large cell with
pseudo-translational symmetry and is a giant pain in the butt to
deal with). I was shooting a
There is another program in CCP4 (from Alexei Vagin) that can generate OMIT
maps. This should allow you to compute
your OMIT map until the fix is introduced. Could be sfcheck but I am not sure
(at home right now).
Fred.
> Message du 03/08/10 21:05
> De : "Hailiang Zhang"
> A : CCP4BB@JISCMAIL
Hi there,
I was using the CCP4-omit to generate the omit maps. However, for 2 input
mtz files with exactly the same colume labels but different system size,
for the small system, it works, but for the large systems, it ended up
with:
./omit: line 9: 8510 Segmentation fault
I am not sure whether
Hi All,
I want thank everyone who replied to my request on Fab:peptide
crystallization. I received wonderful advice from all of you and it was
very helpful in that I did get some beautiful crystals in my screens!
Whether or not there is peptide bound is another matter..:). In case
anyone of you ar
There's no theoretical reason it can't be that long.
BUT it is possible, especially for problematic diffraction
patterns (e.g. from a badly-diffracting, cracked crystal)
for the software to pick some wacky value in its attempt to
fit spots that don't really all belong in the same pattern.
Hi Christian -
As a number of others have pointed out, this unit cell is unusual, but not
impossible. It is, in fact, possible to search the PDB for unit cell
parameters. From the home page, choose "Advanced Search"; on the search page,
choose "X-ray cell dimensions" from the dropdown list of
use fasta
>my_amazing_protein
THISMESSAGESHOULDHAVEBEENSENTTOTHEPHENIXBB
;-)
Preben
On 03/08/2010, at 14.19, Md. Munan Shaik wrote:
> Hi everybody,
> I have a problem with Phenix autobuild. I want to input sequence file
> together with the pdb and mtz that I got from molecular replacement. Bu
Hi Christian
There is nothing uncommon about your cell parameters, take extra care to get
the beam center right during indexing, a few pixels can make all the difference.
gl
Preben
On 03/08/2010, at 13.45, Christian Strube wrote:
> Hi everybody,
>
> indexing of recently collected data gave me u
Hi,
Sorry for the off topic question!
I'm looking at Dali search results and find the molecule names are not
always the same as the ones for the chain identifier from the pdb
entry (maybe the molecule names are always of chain A of the
entries???). I'm wondering if there is a way/tool to extract
Hi everybody,
I have a problem with Phenix autobuild. I want to input sequence file together
with the pdb and mtz that I got from molecular replacement. But I have no idea
which types of sequence files its required. if anybody please help me out.
thanks
=
Totally reasonable, yes. (But when it's that wrong, you easily get it
wrong, too.)
It's probably P6122 or P4122. Be careful to mount your crystals so you
can rotate around the long axis, otherwise you'll never get
non-overlapping data.
phx
On 03/08/2010 12:45, Christian Strube wrote:
Hi
Hi everybody,
indexing of recently collected data gave me unit cell parameters of a=b= 88 and
an extremely long c-axis of 652 A. My question is, if the value of the c-axis
can be reasonable? Or am I wrong with the SG? I know that length doesn't
count, but does anybody has a longer one? Is ther
>
Bei
You can do various statistics, including R-Rfree + resolution from the
PDBeStatistics pages from this link
http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp
Specifically you can do the following for your query, but there are
many other combinations you can try.
Xtal
Received from John Helliwell and thus forwarded to the bb - why should
you miss important information?
Original Message
Subject:Re: [ccp4bb] Accuracy of the position of coordinates
Date: Tue, 3 Aug 2010 09:08:30 +0100
From: John R Helliwell
To: Vellieux Frederi
> I would like to know the accuracy (error) of the position of the
coordinates
This is provided by the output of the refinement software.
An example (CNS-refined structure, from the pdb header, there is an
input file called "xtal_pdbsubmission.inp"
REMARK 3 ESTIMATED COORDINATE ERROR.
RE
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