will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?
Hi, For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot! Best Regards, Hailiang
Hi Hailiang,
For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot!
phenix.tls is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records. phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics. phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors. Pavel.
Hi Hailiang,
For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot!
phenix.tls is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records. phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics. phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors. Pavel.
Thanks Pavel: I tried the following code for PDB 1SX3: ******************* phenix.tls 1SX3.pdb combine_tls=true ******************** but it ended up with: *********** ======================= TLS groups from PDB file header ======================= Sorry: Bad TLS selection: start index > end index. ******************* Not sure whether something wrong with the PDB file or the script. By the way, do I have to specify the selection or phenix.tls will automatically do it based on PDB header? Thanks! Hailiang
Hi Hailiang,
For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot!
phenix.tls
is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records.
phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics.
phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors.
Pavel.
Hi Hailiang,
I tried the following code for PDB 1SX3:
******************* phenix.tls 1SX3.pdb combine_tls=true ********************
but it ended up with:
*********** ======================= TLS groups from PDB file header =======================
Sorry: Bad TLS selection: start index> end index. *******************
yes, the PDB file http://www.pdb.org/pdb/files/1SX3.pdb has the wrong TLS selection: (...) REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 561 D 135 (...) I couldn't find any documentation on this matter, but based on my survey of PDB entries I found that the start_index (561 above) should be less than end_index (135 above), which is not the case for this TLS group.
By the way, do I have to specify the selection or phenix.tls will automatically do it based on PDB header?
The TLS information is extracted from PDB file header automatically. Pavel.
Thanks Pavel! Best Regards, Hailiang
Hi Hailiang,
I tried the following code for PDB 1SX3:
******************* phenix.tls 1SX3.pdb combine_tls=true ********************
but it ended up with:
*********** ======================= TLS groups from PDB file header =======================
Sorry: Bad TLS selection: start index> end index. *******************
yes, the PDB file
http://www.pdb.org/pdb/files/1SX3.pdb
has the wrong TLS selection:
(...)
REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 561 D 135
(...)
I couldn't find any documentation on this matter, but based on my survey of PDB entries I found that the start_index (561 above) should be less than end_index (135 above), which is not the case for this TLS group.
By the way, do I have to specify the selection or phenix.tls will automatically do it based on PDB header?
The TLS information is extracted from PDB file header automatically.
Pavel.
participants (2)
-
Pavel Afonine -
zhangh1＠umbc.edu