Shelxc/d/e require text files (either SHELX hkl or SCALEPACK sca
format), not binary files like mtz.
You can convert directly the XDS_ASCII.HKL from XDS to SHELX hkl with
XDSCONV, which you can then input to shelxc to begin the pipeline. You
still need to supply cell parameters and space group info, though.
I recommend using the hkl instead of the sca file because you can create
an unmerged file with all the measured observations and then you get a
graphical analysis of the anomalous self-correlation. Ideally it should
be very high (>80-90%) at low resolution and should not fall below 30%
below about 2 A resolution. If you don't see this type of curve then it
is highly unlikely that you will be able to solve your structure using
S-SAD. Unless you used a very long wavelength to collect your data (~
2A) the anomalous differences arising from the sulfur atoms are very
small and you need a dataset with very high multiplicity to succeed.
As an alternative, and if your crystals are good enough you can try
soaks with 1M KI before cryocooling your crystal. The iodide ions have a
much higher anomalous signal, even at the Cu K-alpha wavelength, and
even though nearly all sites will be only partially occupied, the
multiplicity requirements are less stringent and it might be enough to
solve your structure.
Em 10/05/2022 13:51, Rituparna Saha escreveu:
Thank you for the suggestions. I had searched the mtzdump in CCP4i,
but didn't find any, I only found the mtz2various program.
I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file
(the one that I had mentioned before) to mtz using Pointless. Then,
when I used this file to run Shelxc/d/e, the job failed and I
encountered errors each time. For this reason, I wanted to view and
analyze the mtz file and HKL file. I donot know how to solve this
problem as well.
Kindly guide me if I went wrong anywhere here.
On Tue, May 10, 2022 at 5:49 PM Pedro Matias <mat...@itqb.unl.pt> wrote:
Hi there,
I assume you processed the data with XDS. If so, you can use
xdsconv to convert the file other formats, including mtz
To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is
a format conversion program, just like xdsconv. You can convert
directly to SCALEPACK format without a USER FORMAT option, and the
output from a .sca file created from an mtz file with MTZ2various
looks like this:
1
-987
105.794 62.940 110.050 90.000 105.008 90.000 c 1 2
1 <-- cell parameters and SG info
-73 1 3 5.1 5.1 7.5 4.5 <--- h,k,l, I+,
sigI+, I-, sigI- (bijvoet mates)
-73 1 4 -1.4 6.8 3.4 5.3
What is the software you are using to solve the structure via
S-SAD? I recomment the shelxc/d/e suite that can be easily run via
the hkl2map GUI.
Best,
Pedro
Em 10/05/2022 12:51, Rituparna Saha escreveu:
Dear all,
I am trying to solve a protein structure via S SAD phasing. I
have the ASCII.HKL file, but whenever I opened the text file I
couldn't understand which one is the F+ and F- values.
Also, how can I read and analyze an mtz file? I tried using the
MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT,
it generated a .sca file, and the text file so generated did not
have any labels (headers) inside it. It just gave me a list of
values.
Kindly guide me through this since I am really a novice in this
field.
--
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-------------------------
Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur
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Regards,
Rituparna Saha
Research Scholar
Bioseparation and Structural Biochemistry Lab
Department of Biotechnology, IIT Kharagpur
--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___________________________________
Phones : (351-21) 446-9100 Ext. 1669
(351-21) 446-9669 (direct)
Fax : (351-21) 441-1277 or 443-3644
email :mat...@itqb.unl.pt
http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL
ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ
Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8
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