[phenixbb] [URGENT] Sorry: Fatal problems interpreting PDB file

[Pavel Afonine]

Hi Esra,

1) running refinement with all default settings

phenix.refine MR.1.updated_refine_002.{pdb,mtz}

works just s expected. So I'm not sure how you get "Sorry: Fatal 
problems interpreting PDB file" message.

2) The data set is overall very incomplete: 63% and per resolution :

    Resolution    Compl
  52.332-12.028   97.09
  11.996-9.598   100.00
   9.540-7.569    98.58
   7.557-6.001    98.47
   6.000-4.760    99.23
   4.758-3.775    98.73
   3.774-2.994    97.20
   2.993-2.374    91.01
   2.374-1.883    68.22
   1.883-1.664    22.61

3) Looks like the model came straight after MR. Is it complete and 
matches the sequence (or, asking differently, does it need some rounds 
of model building before running refinement starts making sense?)?

4) Lot's of atoms in the model has zero occupancy.

All in all, it looks line you are facing a number of typical structure 
solution issues that you need to address first before "fighting with 
R-factors"!

Good luck!
Pavel

On 8/2/23 14:05, Esra A wrote:
> Hello everyone,
>
> I am Esra Ayan.
> I would like to ask you about getting an error in Phenix: *Sorry: 
> Fatal problems interpreting PDB file*
> /
> /
> _I followed the below command to resolve this issue:_
>
> 1. just running "phenix.ready_set MR.1.pdb"
> 2. then running "phenix.refine MR.1.updated.pdb MR.1.mtz 
> MR.1.ligands.cif refinement.input.xray_data.r_free_flags.generate=True
>
> This way, i was able to solve the problem but still getting high Rwork 
> and Rfree values. I still couldn't lower the values even though I 
> tried many ways.
>
> What is your recommendation about this issue?
> i was wondering if I did a mistake by using Step 1 and Step 2 commands.
>
> You can find the reference pdb and mtz files in the attachment.
>
> Any help would be appreciated.
>
> Kind regards,
>
> Esra Ayan
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