Hi Boas,
Yes, tlsanal would work but only if the structure was
refined with the keyword
TLSD waters exclude
either by explicitly including the keyword or
by using a version that of refmac that defaults to
TLSD waters exclude. I believe that recent
versions of refmac 5.6 default to tlsd waters exclude
but that all refmac 5.5 versions (or at least those
after 5.5.0036) default to TLSD water add.
If the structure was refined with TLSD waters add,
then waters have residual B's but since refmac does
not update the TLS ranges to reflect which waters
are in which TLS group, tlsanal cannot add the TLS
component to the waters and you will end up with
a file with full-B on the residues in the TLS
range definition and residual B's on the waters.
My reason for recommending running another refinement
round was that it was less complicated in my mind
then trying to explain the nuances of the effect of
TLSD waters exclude vs TLSD waters add on determining
whether or not tlsanal would be able to properly
convert the file.
Regards,
Mitch
-----Original Message-----
From: Boaz Shaanan [mailto:[log in to unmask]]
Sent: Wednesday, August 03, 2011 1:40 PM
To: Miller, Mitchell D.; [log in to unmask]
Subject: RE: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
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: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Miller, Mitchell D. [[log in to unmask]]
Sent: Wednesday, August 03, 2011 11:14 PM
To: [log in to unmask]
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:[log in to unmask]] On Behalf Of Catarina Silva
Sent: Wednesday, August 03, 2011 12:47 PM
To: [log in to unmask]
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
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