Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Phoebe A. Rice]

In the distant past, we did get some additional phasing signal by a simplified 
version of the RIP concept based on the lability of the bromines in a 
5-bromo-dU substituted DNA in an x-ray beam. 
We collected the peak anomalous signal first and fast, and then just kept 
collecting (we may probably to the edge wavelength too).  If my memory serves 
me right, we binned the data into reasonably complete subsets, and then tested 
which initial - decayed gave us the best difference signal (which would be a 
combination of delta f' and delta f at that point).  We could have solved the 
structure without going to such lengths, but it was kind of fun and it did 
improve the phasing a bit.  And heck, the crystal was in the beam, so why not 
milk it for every smidgen of signal it could provide?


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George Sheldrick 
[gshe...@shelx.uni-ac.gwdg.de]
Sent: Saturday, April 29, 2017 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

Dear Murpholino,

I must apologize, there was a mistake in may last email. The critical
parameter is, as you correctly pointed out, DSCA not RIPW and it is
necessary to try a range of values for DSCA. For this reason I am CCing
this to CCP4bb.

As you will be discovering, RIP phasing is not easy. We treat it like
SIR, but it is complicated by the presence of both positive and negative
difference peaks caused by radiation damage. Also density modification
is less effective for SIR and RIP than for SAD phasing. In the case of
SAD, just replacing negative density with zero improves the phases, but
this is not true of SIR and RIP, However using the anomalous signal as
well (RIPAS) helps, similar to SIRAS.

Best wishes, George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[George Sheldrick]

Dear Murpholino,

I must apologize, there was a mistake in may last email. The critical 
parameter is, as you correctly pointed out, DSCA not RIPW and it is 
necessary to try a range of values for DSCA. For this reason I am CCing 
this to CCP4bb.


As you will be discovering, RIP phasing is not easy. We treat it like 
SIR, but it is complicated by the presence of both positive and negative 
difference peaks caused by radiation damage. Also density modification 
is less effective for SIR and RIP than for SAD phasing. In the case of 
SAD, just replacing negative density with zero improves the phases, but 
this is not true of SIR and RIP, However using the anomalous signal as 
well (RIPAS) helps, similar to SIRAS.


Best wishes, George

--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Weiss, Manfred]

Dear Murph,

the reason we placed more emphasis on data collection and processing
for this tutorial is that the course for which it was created is on data
collection and processing.

With respect to Auto-Rickshaw, we used it as a convenient tool to
check whether the experiment was successful. The nice thing about
Auto-Rickshaw in contrast to other black boxes is, that it tells you
exactly what it did. Which programs it used and which parameters.
As a matter of fact, you will get a text file, which you can paste
directly into the Materials and Methods part of your paper. And
you can use this information to re-do every step and modify as
you please.

Further, an essential part of the tutorial is the diffraction data for
this RIP experiment. Starting from there, you can use of course
any program you like to process and go on from there.

I would suggest that you use the Auto-Rickshaw output as a
rough guideline and try to follow the process and re-do the
individual steps.

If you have question, feel free to ask.

Cheers, Manfred



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Murpholino 
Peligro [murpholi...@gmail.com]
Sent: Friday, April 28, 2017 9:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

That's more like a tutorial for XDS :P (thanks though)

The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the paper 
today) ...
 and
2) my files were not recognized  (MTZ with proper labels ...even the 
XDS_ASCII.HKL files ).

Is it working? Guess I'll try to contact the developers.


Thanks again

2017-04-28 11:29 GMT-05:00 Christian Roth 
mailto:christianroth...@gmail.com>>:

There was a tutorial for MX including UV RIP available from the HZB in Berlin 
(BESSY MX group). Have a look at there website. I'm sure it is still available, 
or maybe they can send you the files on request.

Cheers

Christian


Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:
Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks





Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[George Sheldrick]

Dear Murpholino,

I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP 
phasing (perhaps they should) but you can also run the SHELX programs 
from a command line since you don't like black boxes. SHELXC reads 
XDS_ASCII.HKL files and has some special facilities for RIP, you can 
find them on the SHELX homepage at shelx.uni-goettingen.de -> Wikis & 
manuals -> SHELXC (then go to the end of the page). It is important to 
try several values for RIPW that sets the relative scale of the BEFORE 
and AFTER datasets and can be critical. Under 'SHELX Workshops' you will 
also find a useful account of RIP phasing by Max Nanao from last year's 
ACA Meeting.


Best wishes, George


On 04/28/2017 09:16 PM, Murpholino Peligro wrote:

That's more like a tutorial for XDS :P (thanks though)

The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the 
paper today) ...

 and
2) my files were not recognized  (MTZ with proper labels ...even the 
XDS_ASCII.HKL files ).


Is it working? Guess I'll try to contact the developers.


Thanks again

2017-04-28 11:29 GMT-05:00 Christian Roth >:


There was a tutorial for MX including UV RIP available from the
HZB in Berlin (BESSY MX group). Have a look at there website. I'm
sure it is still available, or maybe they can send you the files
on request.

Cheers

Christian



Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere
on the internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks






--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Murpholino Peligro]

That's more like a tutorial for XDS :P (thanks though)

The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the paper
today) ...
 and
2) my files were not recognized  (MTZ with proper labels ...even the
XDS_ASCII.HKL files ).

Is it working? Guess I'll try to contact the developers.


Thanks again

2017-04-28 11:29 GMT-05:00 Christian Roth :

> There was a tutorial for MX including UV RIP available from the HZB in
> Berlin (BESSY MX group). Have a look at there website. I'm sure it is still
> available, or maybe they can send you the files on request.
>
> Cheers
>
> Christian
>
>
>
> Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:
>
> Hi lads...
> Do you know if there is a good tutorial for doing RIP somewhere on the
> internet?
> What programs can do RIP?
> -SHELX
> -AutoRickShaw
> -?
>
> Thanks
>
>
>

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Christian Roth]

There was a tutorial for MX including UV RIP available from the HZB in 
Berlin (BESSY MX group). Have a look at there website. I'm sure it is 
still available, or maybe they can send you the files on request.


Cheers

Christian



Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the 
internet?

What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks

[ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Murpholino Peligro]

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the
internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks