From: sonali dhindwal
Date: 22 March 2012 12:42
----------
From: Tim Gruene
Dear,
as you open the imosflm-GUI there are three editable fields on top
underneath the top menu which are for the beam position (x,y in mm) and
the detector distance.
As you tell imosflm which images to use, a display window pops open
which allows you to fit circles and mask areas, including the beam stop.
When you let the mouse pointer rest on the icons for a short while a
short description of each icon tells you what they are for - it's all
rather intuitive.
Cheers,
Tim
On 03/22/12 13:42, sonali dhindwal wrote:
> Dear All,
>
> We have collected a data for a protein crystal at SER-CAT Chicago and
> the detector is mar300.We are using mosflm to process the data.While
- --
----------
From: Andrew Leslie
Dear Sonali,
Just to add to Tim's reply, when you open the image with
iMosflm, you can Drag and drop the direct beam position in the
image display window. First, you have to click on the leftmost
icon in the row of icons under the image filename (a green
cross) which will display the direct beam position as read
from the image header as a green cross on the image. You can
then drag then over to where you think the beam position
should be (judging from the position of the backstop shadow).
If indexing still does not work, you can try doing a direct beam search
from the indexing pane, which will do a grid search +/- 2mm from the
current position.
However, you need to beware of one thing. I believe that the rotation axis
on the Sercat beamline goes in the opposite direction to most beam lines.
In such cases, indexing using more than one image will never work, because
the relative phi values will be wrong. You can try indexing with one
image, and then if that works, try predicting the next image. If that
prediction does not match, it is almost certainly because the rotation
direction is wrong.
To deal with this, choose the Settings->Experiment settings menu and click
on the "reverse phi" box. Then you MUST repeat the spot search for each
image being used in indexing, then it should all work.
Best wishes,
Andrew
> D
----------
From: Mark J van Raaij
If you are lucky (or should I say unlucky) and have an ice-ring on the same image or on another image collected during the same shift and similar distance, you can estimate the beam centre using the "fit circle" option.
Although software (and beamlines) have improved greatly, it can still be a good idea to collect ice- or wax-rings on purpose before or after data collections for determining accurate beam centres.
Mark J van Raaij
Date: 22 March 2012 12:42
| Dear All, We have collected a data for a protein crystal at SER-CAT Chicago and the detector is mar300. We are using mosflm to process the data. While indexing, the beamstop which it is taking is wrong, due to which it fails.I am trying to define the beamstop manually using tools like mask and spot search area. (it might be wrong) It will be highly appreciable if someone can please suggest if this the method we should use to define the beamstop or there is any site definition file which has to be used, as it is available for HKL2000 or how we have to define the beamstop in mosflm. -- Sonali Dhindwal "Live as if you were to die tomorrow. Learn as if you were to live forever." |
----------
From: Tim Gruene
Dear,
as you open the imosflm-GUI there are three editable fields on top
underneath the top menu which are for the beam position (x,y in mm) and
the detector distance.
As you tell imosflm which images to use, a display window pops open
which allows you to fit circles and mask areas, including the beam stop.
When you let the mouse pointer rest on the icons for a short while a
short description of each icon tells you what they are for - it's all
rather intuitive.
Cheers,
Tim
On 03/22/12 13:42, sonali dhindwal wrote:
> Dear All,
>
> We have collected a data for a protein crystal at SER-CAT Chicago and
> indexing, the beamstop which it is taking is wrong, due to which it
> fails.
>
> I am trying to define the beamstop manually using tools like mask and
> spot search area. (it might be wrong) It will be highly appreciable
> if someone can please suggest if this the method we should use to
> define the beamstop or there is any site definition file which has to
> be used, as it is available for HKL2000 or how we have to define the
> beamstop in mosflm.
>
>
>
- --> fails.
>
> I am trying to define the beamstop manually using tools like mask and
> spot search area. (it might be wrong) It will be highly appreciable
> if someone can please suggest if this the method we should use to
> define the beamstop or there is any site definition file which has to
> be used, as it is available for HKL2000 or how we have to define the
> beamstop in mosflm.
>
>
>
- --
----------
From: Andrew Leslie
Dear Sonali,
Just to add to Tim's reply, when you open the image with
iMosflm, you can Drag and drop the direct beam position in the
image display window. First, you have to click on the leftmost
icon in the row of icons under the image filename (a green
cross) which will display the direct beam position as read
from the image header as a green cross on the image. You can
then drag then over to where you think the beam position
should be (judging from the position of the backstop shadow).
If indexing still does not work, you can try doing a direct beam search
from the indexing pane, which will do a grid search +/- 2mm from the
current position.
However, you need to beware of one thing. I believe that the rotation axis
on the Sercat beamline goes in the opposite direction to most beam lines.
In such cases, indexing using more than one image will never work, because
the relative phi values will be wrong. You can try indexing with one
image, and then if that works, try predicting the next image. If that
prediction does not match, it is almost certainly because the rotation
direction is wrong.
To deal with this, choose the Settings->Experiment settings menu and click
on the "reverse phi" box. Then you MUST repeat the spot search for each
image being used in indexing, then it should all work.
Best wishes,
Andrew
> D
----------
From: Mark J van Raaij
If you are lucky (or should I say unlucky) and have an ice-ring on the same image or on another image collected during the same shift and similar distance, you can estimate the beam centre using the "fit circle" option.
Although software (and beamlines) have improved greatly, it can still be a good idea to collect ice- or wax-rings on purpose before or after data collections for determining accurate beam centres.
Mark J van Raaij
----------
From: sonali dhindwal
| Dear Andrew and all the people for their help, I am providing mosflm the right beamstop and now, I am able to do the indexing, refinement and indexing too. Then I run scala for the output mtz file and it shows Rmerge too high 0.58 and also when examining the spots and predictions in the image, it seems like it is not picking a lot of spots, so missing large number of reflections. So, any suggestions to correct it or am i doing something wrong. Thanks again for the help and suggestions -- Sonali Dhindwal "Live as if you were to die tomorrow. Learn as if you were to live forever." -- |
----------
From: Francis E Reyes
What resolution are you working at? What are the unit cell dimensions?
On Mar 22, 2012, at 11:10 AM, sonali dhindwal wrote:
> Dear Andrew and all the people for their help,
>
> I am providing mosflm the right beamstop and now, I am able to do the indexing, refinement and indexing too.
> Then I run scala for the output mtz file and it shows Rmerge too high 0.58
> and also when examining the spots and predictions in the image, it seems like it is not picking a lot of spots, so missing large number of reflections.
F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
----------
From: Andrew Leslie
Hi Sonali,
How did you assign the spacegroup ... did you run POINTLESS ?
A table of Rmerge vs resln from SCALA would be helpful in addition to a
screen shot of an image as Francis suggested.
Andrew
> Dear Sonali,
>
> Â Â Â Â Â Â Just to add to Tim's reply, when you open the image with>
>> indexing, the beamstop which it is taking is wrong, due to which it
>> fails.
>>
>> I am trying to define the beamstop manually using tools like mask and
>> spot
>> search area.
>> (it might be wrong)
>> It will be highly appreciable if someone can please suggest if this the
>> method we should use to define the beamstop or there is any site
>>Â definition file which has to be used, as it is available for HKL2000>>
>> I am trying to define the beamstop manually using tools like mask and
>> spot
>> search area.
>> (it might be wrong)
>> It will be highly appreciable if someone can please suggest if this the
>> method we should use to define the beamstop or there is any site
>> or
>> how we have to define the beamstop in mosflm.
>>
>>
>>
>> --
>> Sonali Dhindwal
>>
>> “Live as if you were to die tomorrow. Learn as if you were to live>> how we have to define the beamstop in mosflm.
>>
>>
>>
>> --
>> Sonali Dhindwal
>>
>> forever.â€
>
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