Yes - Prasun - I think self rotation functions are a validation tool rather
than a preliminary piece of evidence..
Sometimes it helps to know one expects a trimer or a 13 fold axis or some
such but in this case they can help tell you you have the right solution -
once you have it!
All the best
Hi Eleanor
According to the peak search the 3 highest peaks on the chi=180 section are
at:
| 390.00 -52.26 180.000.49 |
| 490.00 -73.73 180.000.47 |
| 590.00 -66.55 180.000.44 |
plus a lot of lower peaks on that section which are clearly in
Ian - I read the log file - agree, you cant get much from the pictures..
But the peak heat of the translation vector is 50% od the origin - ie
pretty strong..
And ditto for the rotation angles - all 50% of origin too
But of course any set of rotation angles does not have to generate a closed
Hi Eleanor
On Sat, 22 May 2021 at 14:55, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> And several strong rotations
> 180 0 90. - ie a 4 fold round the c axis?
> 0 0 60 - ie a 6 fold round the c axis?
>
How can you tell that from the meagre information provided
First Q - how good is your data - is there no possibility of twinning
or any other distraction?
Second Q - To compare those results properly we need to know how the
P2 and the P222 cell align - are the cell dimensions more or less the
same?
But the 2 plots you attach (and the list above) show
Dear CCP4 Users,
In Phenix.xtriage and phaser, the analyses of the
Patterson function reveals a significant off-origin peak that is 23.25
% of the origin peak, indicating pseudo translational symmetry at
frac. cord. vector 0.0000.5000.022 . It did not indicate any
twinng.
a script for it, it is very little work.
Good luck!
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Monica
Mittal
Gesendet: Montag, 18. November 2013 14:37
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] SELF-ROTATION FUNCTION FROM
Well - translation peaks are listed in the data processing log file - look for
the word translation. If there is an off-origin peak 25% of the origin you
probably have two 9or more) molecules in similar orientations but displaced
from each other.
Self rotation peaks are listed in various
*Dear All
*In case we have more than one molecule per asymmetric unit, how to look
for the results of the self-rotation function calculation and translation
peak in the native patterson.
--
Regards
Faisal
School of Life Sciences
JNU
Emma,
You need to provide more information. Luckily, I222 is orthorhombic, so a* is
along a, b* is along b, and c* is along c. This makes things so much easier to
interpret. I hope the plotting conventions you used are typical: b along +y
(North pole), a along +x (to the right), and c
Did you perform Matthews analysis? It should give you some indications
on the number of monomers in the asymmetric unit. Can you send the list
of peaks? It should be a file with .tab extension.
Cheers
Fulvio Saccoccia
Dept. of Biochemical Sciences
Sapienza University of Rome
Il 10/02/2013
On 06/03/2011 02:01 PM, Careina Edgooms wrote:
Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy
*Subject:* Re: [ccp4bb] self rotation function
Hi Careina
30% of the origin peak is fairly respectable. You could probably make it
higher by varying the high res cutoff. You have 2 Ang: it may be that the
NCS doesn't extend to that resolution, so making it a bit lower might
improve the signal
Hi Careina
30% of the origin peak is fairly respectable. You could probably make it
higher by varying the high res cutoff. You have 2 Ang: it may be that the
NCS doesn't extend to that resolution, so making it a bit lower might
improve the signal/noise ratio. It would be nice to see the plot
Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy of
the file. If someone could assist me to
You need to tell us the spacegroup for us to be very helpful...
And I often find the molrep plots less useful than the list of peaks and
all the symmetry equivalents..
(It has a weird name - *rf or *doc I think)
But I guess all the variant are in point group P222? There are the 3
expected 2
Hi Sympath,
Did you try to change the default Search radius?
To my understanding MOLREP estimats the search radius somehow from the
volume of the asymmetric unit and not from the expected radius of the
monomer (you don't give the program the number of expected molecules).
The signal of the SRF
Dear All,
Thank you very much for the reply and suggesions regarding my self rotation
function calculation. Really I appreciate who are all responded me regarding
my query. Now I got some idea about my structure in the assymetric unit.
Thanking you once again.
Sincerely yours,
Sampath
On Thu,
Hi Sampath,
We had a very similar case, an octamer (422 symmetry) in C2 space group.
What saved us for solving the structure (and by the way interpreting the
self-rotation function !!) was a low resolution electron microscopy
envelope (silver stain and cryo-EM) that gave us the organisation of
U Sam wrote:
Hi,
I am using a native data of 2 angstrom and C2 space group, final R-merge is
0.059. I processed data using HKL2000.
I highly appreciate suggestion how can I generate self-rotation function, get figures and save that in required format.
Thanks, Sam
Hi,
I am using a native data of 2 angstrom and C2 space group, final R-merge is
0.059. I processed data using HKL2000.
I highly appreciate suggestion how can I generate self-rotation function, get
figures and save that in required format.
Thanks, Sam
Hi Eleanor and others:
This is a little too late to follow up on this thread. But here is a
similar question concerning MR and self-rotation.
Without going into the translational part of MR, is it possible to tell
the orientation of a 2-fold axis directly from the cross-rotation peaks?
e.g. I
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