Dear Colleagues,
When I processed one data set with XDS, the index step said there is no
sufficient (<50%) spots indexed, however after I tried various parameters
to get the same cell unit and space group, I chose to ignore this message
and wen on to integration.
During the integration I had to
Dear All,
I have a MR case which may contain two different molecules, ideally 1:1
ratio. Solvent content analysis indicates most likely to be 4~6 hetero
molecules. The data shows at least 5 strong translational NCS vectors.
When I tried to run PHASER, it always said "correction factors NOT
applie
that, but it's possible.
>
> Phil Jeffrey
> Princeton
>
>
> On 11/14/13 5:22 PM, Niu Tou wrote:
>
>> Dear All,
>>
>> I have a strange MR case which do not know how to interpret, I wonder if
>> any one had similar experiences.
>>
>> The o
;
> Melanie
> ----------
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [
> niutou2...@gmail.com]
> *Sent:* 14 November 2013 23:58
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Weird MR result
>
> Dear Phil,
>
&
Dear All,
Does any one know how to strictly fix the cell dimensions during data
processing? In HKL2000 there is only a keyword to define the longest
vector. In XDS there is a option to input cell parameters, but sometimes
the program would not follow the input values
and switch back to the one it
ers will ensure that you
> still get a good prediction of spot positions.
>
> I suspect that this can be done in other programs too.
>
> Without knowing why you want to do this, I cannot comment on whether this
> is the best procedure to follow.
>
> Best wishes,
>
> A
Dear All,
Does any body know if the existence of pseudo translation symmetry will
affect refinement ? If it does, is there any keyword or method to avoid it?
Thanks!
Best,
Niu
Dear All,
Recently we collected some data of a MBP fusion protein, at around 4A
resolution. The protein itself is about half of the MBP size. However when
we tried to solve it with MR, it failed. We tried to use MBP alone,
homology model of target protein alone, and MBP+model. It is very strange
t
Dear All,
I have a ccp4 format map file in P1 spacegroup, I would like to manipulate
it in several ways:
1. enlarge the cell dimension . When I tried "CELL" keyword in MAPMAN, the
density scaled up together with the cell dimension. Does anybody know how
to do it without changing the density?
2.
Dear Collegues,
Does anybody know how to use the server http://checkcif.iucr.org/? I have
downloaded structure factor and structure model cif files of a structure
from PDB. However it looks this server only accept one single file, it does
not work if these two files are uploaded separately. My ques
Dear Colleagues,
I am trying to repeat a series termination effect calculation displayed as
figure 2 in a publihsed paper
(http://www.ncbi.nlm.nih.gov/pubmed/12215645). Formula
(1) was used to implement this calculation. Since f(s) is not defined in
detail in this paper, I used formula and paramet
Dear colleagues,
Is there any program can rotate a density map (generated by FFT, could be
read in Coot and Pymol) given the matrix? I have tried
Extension->Maps-> Transform map by LSQ model fit, it looks doesnot work.
While the program Edit/Rotate map & Mask in CCP4 gave an error message:
mapmask
Dear Colleagues,
Does anybody know if the definition of rotation parameters in Maprot are
different from that of Coot? I used Coot to superimpose a model A to model
B, to get a new model A* and rotation parameters (Euler angles and
translations), howerver when I used these parameters to move the o
Hi colleagues,
We have collected several datasets at APS with detector 24IDE, while
processing date, the beam center is obviously not in position. But no
matter what values we set in "Site Configuration" or "def.site", it remains
about (156, 165). Based on the image, the estimated correct center s
Dear colleagues,
We have some diffraction data from small peptide crystals, the shape of
diffraction spots looks normal, and resolution is beyond 2A. The data were
collected with 5 degree rotation per image. Later on we found it is hard to
do index. Does anybody know some skills to figure this pro
t;
> in XDS I would check the output of IDXREF.LP to figure out if indexing
> seems possible, i.e. if the input parameters seem stable or if they
> are just floating around
>
> and many more - it depends on the data set, really!
>
> Best,
> Tim
>
> On 03/13/2013 09:12 PM,
Dear All,
Is there any command can set the resolution limit for index step in XDS? I
only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a
definition of resolution range after index step
as it says:
INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by
DEFPIX,INTEGRATE,CORRECT
Than
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