[sharp-discuss] how to add native to MAD?

[Claus Flensburg]

Hi,

to add a new compound with S-atoms for the native follow these steps:

If your MAD.data.mtz file does not contain columns with the native
generate one and lets call it MADNAT.data.mtz (place it in your
sharpfiles/datafiles directory).

Also prepare an NAT.hatom file containg lines like these:
ATOM S   0.73262   0.35117   0.90679
ATOM S   0.33773   0.05688   0.21465
ATOM S   0.84311   0.25314   0.11210
ATOM s   0.56008   0.71903   0.01215
This file should also be placed in the sharpfiles/datafiles directory.

Launch the SIN file editor starting from your last MAD results, then:

1) In the "Global Information Editor" select the correct MADNAT.data.mtz file.
2) Possibly change the project name to: MADNAT
3) Under Table of Contents (ToC) click on G-site(s)
4) Under 2. Add heavy atom sites from file: NAT.hatom
5) Under Table of Contents (ToC) click on C-1
6) At the top "Help New Delete Submit ..." click on New
7) Click on the just created Compound C-2
8) Say "Create 4 new C-site(s) of type S ..." starting from the
   approriate G-site number.
9) Set the appropriate values for the X-1, W-1, and, B-1 as usual.

Submit the job.

With best wishes,

ClAuS


On Fri, Sep 26, 2003 at 10:28:20AM -0700, Sarah Gillmor Hymowitz wrote:
> Dear colleagues,
> I want to refine phases using the MAD+native scenario.  I have mediocre
> NABR 3.5 A phases and would ike to try to add information about my
> native data  (using the NABR phases, I have located 4 sulfers in my asu
> and would like to include any phasing from teh sulfer anom signal at
> 1.85A).  I have successfully used autoSHARP and SHARP to refine, phase
> imrpove etc the MAD data.  I have not been able to add the native data.
> I am starting sharp based on my final round of MAD phase refinement but
> I can't seem to generate the additional "C-2" entry in the TOC.  I read
> the manual and it seems like it should be intuitively obvious what ot do
> but I can't figures it out.  I have tried adding additional G and C
> sites but that doesn't generate any new entry in the TOC where I can
> imput the new column info, wavelenght, atom locations etc.
> 
> What am I doing wrong?
> 
> Thanks
> Sarah Gillmor Hymowitz
> Genentech
> 
> 
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