Dear Catarina,
When TLS is involved in refinement using a script, the keyword "tlsout
addu" should be added to produce a coordinate file containing the full B
factor. The latest REFMAC interface (in CCP4i) has a button "Add TLS
contribution to XYZOUT" in the folder of TLS Parameters which will add
this keyword.
There are three ways to convert file so it contains full B factors:
1. You can convert your PDB file so it contains full B factors using the
server at http://deposit.rcsb.org/adit/REFMAC.html
2. Convert locally using the script at
http://deposit-beta.rcsb.org/tlsanl/tlsanl_script.csh
Run tlsanl_script.csh pdbfile
(note: CCP4 should be installed on your local machine prior to running
the script)
3. Convert using CCP4i package
* Find the file of TLS parameters TLSOUT that corresponds to the
coordinate file, or if necessary extract the TLS parameters from the PDB
file using the CCP4 program tlsextract
* Use CCP4's tlsanl to put the full B factor in the PDB coordinate file,
available in the GUI interface as the task "Analyse TLS parameters". Be
sure to set the keyword BRESID T in this interface.
Please let us know if we can be of any further help.
Sincerely,
Rachel Green
***************************************************
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
__________________________________________________
PDB 40: Celebrate four decades
of innovation in structural biology
Oct 28-30, 2011 at Cold Spring Harbor Laboratory
http://meetings.cshl.edu/meetings/pdb40.shtml
**************************************************
On 8/3/2011 1:47 PM, Catarina Silva wrote:
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
