[phenixbb] phenix.real_space_refine crashes for very large pdb files

[Pavel Afonine]

Hi Tofayel,

> My phenix.real_space_refine run crashes with the error mentioned below 
> when I have used following command to run it on a complete ribosome 
> (containing coordinates for small subunit and large subunit in a 
> single pdb file):
>
> phenix.real_space_refine model.pdb map.mrc resolution=4.5 
> reference_coordinate_restraints.enabled=true 
> reference_coordinate_restraints.selection="chain A and resseq 2:700" 
> reference_coordinate_restraints.sigma=0.05 
> secondary_structure.enabled=True res.eff > out.out
>
>
> From the out.out file I can see that, it ran for 5 macro_cycles and 
> started group b-factor refinement which reads (last few lines):
>
>
> |-----------------------------------------------------------------------------|
> |-group b-factor refinement (macro cycle = 0; iterations = 
> 0)-----------------|
> | r_work = 0.3809 r_free = 0.3809 target = 0.153923 restraints weight 
> = None  |
> |-----------------------------------------------------------------------------|
> |-group b-factor refinement (macro cycle = 1; iterations = 
> 32)----------------|
> | r_work = 0.3687 r_free = 0.3687 target = 0.144348 restraints weight 
> = 1067.479|
> |-----------------------------------------------------------------------------|
> |-group b-factor refinement (macro cycle = 2; iterations = 
> 37)----------------|
> | r_work = 0.3724 r_free = 0.3724 target = 0.147257 restraints weight 
> = 482.176|
> |-----------------------------------------------------------------------------|
> |-group b-factor refinement (macro cycle = 3; iterations = 
> 32)----------------|
> | r_work = 0.3747 r_free = 0.3747 target = 0.149066 restraints weight 
> = 262.900|
> |-----------------------------------------------------------------------------|
>
> The run crashes at this point....
>

It crashes trying to refine B-factors in reciprocal space (which is not 
the best idea anyway, I mean using reciprocal space for this, but that's 
at we have at present!).
So, please disable B factor refinement by adding this to your command 
line: "run=minimization_global" (by default it is 
"run=minimization_global+adp").

> However, phenix.real_space_refine runs fine when I am 
> refining a protein chain or a complex (for eg: just the large or 
> the small subunit of a ribosome). Does it have to do with my pdb file 
> being so big after merging of both subunits where I have also crossed 
> 99999 atoms and atom serial numbers start from A0000?
>

No, it has nothing to do with this.

> A related question: What is the latest consensus of using chain IDs 
> and atom serial numbers to use in phenix.real_space_refine for 
> handling large files like ribosome pdbs ? I have found some 
> information on: http://cci.lbl.gov/hybrid_36/
>

Using hybrid36 and two-letter chain IDs allows to fit into PDB virtually 
any size model. Such files work fine across Phenix and some good 
graphics programs. But PDB would not like these files. Since PDB files 
will go away anyway with mmCIF being replacement, I'd say best is to use 
mmCIF that can fit any size models too and are supported in/out across 
Phenix.

Tools to convert PDB <> mmCIF:

phenix.cif_as_pdb
phenix.pdb_as_cif

Please let us know should you have more questions or need any help!

Pavel

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