I would run DM first to extend the experimental phases to the limit of
your resolution..
Then if you run REFMAC to refine your MR model, using the experimental
phases as part of the input the output phases from REFMAC will include
contributions from both the MR and the DM/experimental phasing. Thi
---
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
> *David Veesler
> *Sent:* Tuesday, July 12, 2011 9:21 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] how to combine the experimental phase and
> molecular replacement phase
&g
CP4BB@JISCMAIL.AC.UK] On Behalf Of David
Veesler
Sent: Tuesday, July 12, 2011 9:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to combine the experimental phase and molecular
replacement phase
Hi Jiamu,
to complete the Juergen answer, that's true that the MR-SAD approach is very
po
structure, and refined simultaneously, the phase information is combined
naturally, without having to export part of
the information through Hendrickson-Lattman coefficients.
I am very happy to see that phenix and phaser have adopted and are
promoting using the SAD function. Although, I
Hi,
Most of the answers are interpreting your question as follows, that you have a
single Se-SAD data set that goes to 3.3A but only has anomalous signal to 3.8A.
Is that correct? If so, then there are various ways to combine the MR and SAD
phase information. As you might imagine, we like th
Dear Jiamu,
Try out MRSAD protocol of Auto-Rickshaw
(http://www.embl-hamburg.de/Auto-Rickshaw). You can start this just by
providing your selenomet
data, starting model, sequence information and space group on the
Auto-Rickshaw server. It would do substructure determination based on
your
Hi Jiamu,
OASIS may help solving your problem. We have example on solving an
originally unknown protein (1086 residue in the AU) at 3.3A resolution with
Se-SAD data (redundancy=3.3). The process involved SAD-iteration and
MR-iteration with OASIS. If you need help, we can discuss off list.
Cheers
You can use Refmac to take your SAD information (F+ and F-), heavy atom
and MR model directly and refine both your Se sites and your MR model
simultaneously. This function in Refmac has been around for 'more years'
and is what has been re-implemented in a mathematically equivalent form in
Phas
Hi Jiamu,
to complete the Juergen answer, that's true that the MR-SAD approach is very
powerful and can definitely help in your case. You can use Sharp and add the
information from your partial molecular replacement solution encoded as HL
coefficients and do a MR-SAD phasing.
Here is the procedu
Hi Jiamu,
this program can do it:
http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm
Let me know if you have questions and we can discuss it (off-list).
Pavel.
On Tue, Jul 12, 2011 at 6:08 PM, Jiamu Du wrote:
> Dear All,
> I am now working on a low resolution phase determ
http://www.globalphasing.com/sharp/
or you could extend your phases using DM if you have more than one molecule in
the asu.
I'm sure there is also a way to convince solve/resolve to do what you want.
If you see enough in your map, just build a backbone model and use that to
generate a crude mask
On Tue, Jul 12, 2011 at 6:08 PM, Jiamu Du wrote:
> I am now working on a low resolution phase determination (around 3.3 A with
> Se anomalous signal around 3.8 A).
> I can find the Se site and get the phase, but the density map is not so
> good.
> Some part of the protein (about 1/3) has a homolo
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