DNA and SASREF

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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jtrewhella
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Joined: 2016.10.27 23:51

DNA and SASREF

#1 Post by jtrewhella » 2016.10.28 00:00

I have a protein-DNA complex that I am trying to model fit to an X-ray scattering curve and SASREF appears to be jumbling the DNA coordinates. They read into pymol perfectly sensibly (attached), but when I run SASREF locally, the output model has completely jumbled DNA sequence. When I try to run the job in ATSAS on-line (see attached zip file), it consistently fails with the error message:
"Errors and/or warnings registered during execution:
find: `*.fit': No such file or directory that is has been unable to find a *.fit"

many thanks for your assistance in advance, jt
Attachments
CZ38DNA1.zip
failed job in atsas on-line version
(56.93 KiB) Downloaded 146 times
optiX_mGCG_py.pdb
this is the DNA coord file
(88.2 KiB) Downloaded 148 times

SaxsMax
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Posts: 349
Joined: 2007.08.03 19:16

Re: DNA and SASREF

#2 Post by SaxsMax » 2016.11.04 13:22

Online Sasref has actually the problem with
CZ38_ZF8_ZN_KE-TG.pdb file which has a line
"HETATM 248 ZN ZN _ 1 3.166 1.522 -4.762 1.00 0.55 ZN"
The line contains a special tab character and cannot be read.
Please replace it with
"HETATM 248 ZN ZN _ 1 3.166 1.522 -4.762 1.00 0.55 ZN"
I have edited this file in CZ38DNA1 folder and restarted the job.

SaxsMax
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Posts: 349
Joined: 2007.08.03 19:16

Re: DNA and SASREF

#3 Post by SaxsMax » 2016.11.04 13:48

As for DNA, its sequence does not change in Sasref, but both strands get the same chain id

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