[phenixbb] Refmac error using PDB coordinates generated by Phenix PDB File Editor

Xiao Lei xiaoleiusc at gmail.com
Fri Apr 29 13:42:56 PDT 2016


Hi Phenixbb members,

I'm using Phenix PDB File Editor under Phenix GUI "Model Tool" to change
occupancy of two short 7 polyalanine alpha helix peptide chain (chain I and
K, placed in reverse orientation of each other in one region (or density
blob) of my model, each chain half occupancy) , I can change the occupancy
very easily with the tool, but I have two types of errors using the
coordinates generated by the tool in Refmac.

1. If I set chain ID of chain K to chain I with the same residue number
with half occupancy but in reverse order (Chain I, Ala7th--13th 0.5
occupancy and Chain I, Ala7th--13th 0.5 occupancy) , Refmac could not
refine the model with an error message below:
 I am reading library. Please wait.
                mon_lib.cif
  ERROR : ALA              : duplicated atom_name : "N   ".
          chain: II   residue:    7
  ERROR : ALA              : duplicated atom_name : "CA  ".
          chain: II   residue:    7
  ERROR : ALA              : duplicated atom_name : "CB  ".
          chain: II   residue:    7
  ERROR : ALA              : duplicated atom_name : "C   ".
          chain: II   residue:    7
  ERROR : ALA              : duplicated atom_name : "O   ".
          chain: II   residue:    7
 IERR =            1

There is an error. See above
===> Error: Fatal error. Cannot continue.

I understand Refmac can not allow two peptide chain with the same ID and
residue number if both peptides are full occupancy (1), but why in this
case even half occupancy of the same chain ID and residue number is not
tolerated?

2. If I set chain ID of chain K and chain I half occupancy (Chain K,
Ala7th--13th 0.5 occupancy and chain I, Ala7th--13th 0.5 occupancy) , put
chain K and chain I in the same density blob with reverse direction, and
run Refmac, this time Refmac can finish but gave me error message in log
file as below:
  I am reading library. Please wait.

                mon_lib.cif

  INFO:     link is found (not be used) dist=   1.486 ideal_dist=   1.240

            ch:II   res:   7  ALA              at:N   .->ch:KK   res:  11
 ALA              at:O   .

  INFO:     link is found (not be used) dist=   1.625 ideal_dist=   1.080

            ch:II   res:   8  ALA              at:O   .->ch:KK   res:   9
 ALA              at:O   .

  INFO:     link is found (not be used) dist=   1.584 ideal_dist=   1.400

            ch:II   res:  10  ALA              at:N   .->ch:KK   res:  11
 ALA              at:N   .

  INFO:     link is found (not be used) dist=   1.397 ideal_dist=   1.530

            ch:II   res:  10  ALA              at:CB  .->ch:KK   res:  11
 ALA              at:CB  .

  INFO:     link is found (not be used) dist=   1.153 ideal_dist=   1.400

            ch:II   res:  11  ALA              at:N   .->ch:KK   res:  10
 ALA              at:N   .

  INFO:     link is found (not be used) dist=   1.820 ideal_dist=   1.524

            ch:II   res:  11  ALA              at:CA  .->ch:KK   res:  10
 ALA              at:CB  .

  INFO:     link is found (not be used) dist=   0.888 ideal_dist=   1.530

            ch:II   res:  11  ALA              at:CB  .->ch:KK   res:  10
 ALA              at:CB  .

  INFO:     link is found (not be used) dist=   1.808 ideal_dist=   1.530

            ch:II   res:  12  ALA              at:CB  .->ch:KK   res:   9
 ALA              at:CB  .

  INFO:     link is found (not be used) dist=   1.764 ideal_dist=   1.400

            ch:II   res:  13  ALA              at:N   .->ch:KK   res:   7
 ALA              at:N   .

  --------------------------------
I do not know why Refmac gave me this message, is it because the two helix
chain (I and K) are placed in the same region, even though both with 0.5
occupancy of both chain, Refmac still automatically tries to connect the
main chain atom between two different chains (I and K) because main chain
atoms are placed too close to each other (Refmac think there is a link
between them?) ?


3. In summary, should I use Phenix Refine instead of Refmac to handle the
pdb coordinates generated by Phenix PDB file editor because Phenix Refine
may have better compatibility?

Thanks in advance.
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