[sharp-discuss] about some warnings

[Ditlev Egeskov Brodersen]

Hi DeQiang Yao,

  those warnings are simply to check that you know what you are doing and
shouldn't affect the end result (SHARP developers please correct me if I'm
wrong).

  1) SHARP always complains about an undefined molecular weight if you only
enter the no. of residues, which is a bit annoying, I agree. I think what it
is trying to say is that the calculated molecular weight will be based on
110 Da/residue or whatever and thus not be completely correct.

  2) Same as above: If you only give the wavelength and element, SHARP will
have to take the f' and f'' from the table, which potentially can deviate
from the observed values. But for sulphur off the edge at 1.54Å you should
be fine as a first approximation. You can always refine them later anyway
(keep f' fixed for first wavelength).

  3) This is slightly more puzzling, because I assume that you entered the
correct number of atoms corresponding to 2 molecules in the asu? I think
what may be happening is that autoSHARP checks the Matthews' coefficient and
decides (wrongly) that there's only 1 molecule, then concludes (based on the
sequence you supplied) that there can be a max. of 11 sulphurs.

  In other words: I would just carry on and ignore the warnings for now.

Regards,

  Ditlev Brodersen

---

Ditlev E. Brodersen, Ph.D.
Associate Professor, Forskningslektor

Department of Molecular Biology   Office:  +45 89425259
University of Aarhus              Lab:     +45 89425022
Gustav Wieds Vej 10c              Fax:     +45 86123178
DK-8000 Aarhus C                  Email:   deb at bioxray.dk
Denmark                           Lab WWW: http://bioxray.dk/~deb

-----Original Message-----
From: sharp-discuss-bounces at globalphasing.com
[mailto:sharp-discuss-bounces at globalphasing.com] On Behalf Of DeQiang Yao
Sent: 19. juli 2005 09:03
To: sharp-discuss at globalphasing.com
Subject: [sharp-discuss] about some warnings

Dear sir,
When I run autoSHARP, there will be some warnings.
The warning as follow,


* No molecular weight
You haven't defined the molecular weight! Automatically set to
calculated value 40522 Da. (based on number of residues = 402)

* No f'/f'' values (wavelength 1, w1, atom S) 
No f'/f'' values defined for atom of type "S" in wavelength 1:
           automatically set to calculated values for wavelength
           1.5418 Å (0.3173,0.5576)

*  mismatch between no. of sites and sequence  
you specified to search for 22 heavy atom sites of type S - but the
most likely number of monomers (1) together with the sequence ( Met
and Cys residues per monomer) suggest that you should be looking for
11 sites!

1)I define the number of residues and the sequence but no molcular weighting
is
provided.
2)The wavelength is given but f'/f'' is not.
3)There are 22 heavy atoms in two molecule per asymmetry unit. I have find
20 of
them by SHELXD and write them in ***.hatom. 

Can these warnings affect the result? Is there anything wrong?
Thanks in advance.

Best regards
DeQiang Yao



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