Just wondering: wouldn't running tlsanal on the final refmac output as Catarina
has it now put the true aniso record straight?
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [email protected]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[email protected]] on behalf of Miller, Mitchell
D. [[email protected]]
Sent: Wednesday, August 03, 2011 11:14 PM
To: [email protected]
Subject: Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Hi Catarina ,
For your final refmac refinement job, you need to include
the keyword
TLSO ADDU
to have the TLS contribution added to the residual B-factors.
This keyword can also be set from the recent version of the ccp4i
GUI by checking the checkbox for "Add TLS contribution to XYZOUT"
in the TLS section.
(This addu output file is needed for deposition but should not be
used for further TLS refinement with refmac).
Also, depending on the version of refmac you are using, it may also
default to adding waters to TLS groups. If it does, then they
waters will have ANISOU records after TLS refinement. Note that
refmac does not update the TLS range records to reflect this change.
If you want to exclude water from TLS assignment, you can
also include the "TLSD waters exclude" keyword.
Regards,
Mitch
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Catarina
Silva
Sent: Wednesday, August 03, 2011 12:47 PM
To: [email protected]
Subject: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Dear all,
I am trying to deposit a pdb containing TLS groups. PDB instructions states:
"As we have mentioned on the start page for autodep, entries refined using
REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM
records, with the TLS contribution coded into ANISOU records."
I did run Refmac with TLS parameters and, as such, I would expect that all the
values necessary to pdb deposition would be on the pdb coming out from refmac.
However, when I deposit the pdb a 'serious error' comes up, not allowing me to
deposit the coordinates:
"You will NOT be allowed to proceed for deposition unless these issues are
corrected.
TLS and ANISOU/RESIDUAL B-FACTORS.
As we have mentioned on the start page for autodep, entries refined using
REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM
records, with the TLS contribution coded into ANISOU records.Your entry
contains TLS records but no ANISOU records OR Residual B-factors. Please
correct this and reupload your structure for validation"
I don't really understand why these supposed missing values are not already
contained in the pdb file, and I can't figure out how to get them. Does anyone
knows how to fix this situation?
Thanks in advance!
Catarina Silva
