[phenixbb] Real space refinement of complete virus structure

Pavel Afonine pafonine at lbl.gov
Tue Mar 13 04:03:51 PDT 2018

Hi Tofayel,

> I am trying to refine a complete virus pdb structure (possessing 
> icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. 
> The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not 
> supported". So, I followed a previous post in phenixbb: 
> http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html 
> and merged multiple models into one

perhaps the advice you quote above is getting outdated a bit (though 
still valid!). Yes, most Phenix tools can't do much with multi-model 
files. In your case you can convert your multi-model file into a one 
model file where all the models become new chains.


should do it for you.

> but faced following problems:
> 1. This merged file is unreadable in UCSF Chimera.

I guess you better talk to Chimera developers unless it is clearly fault 
of Phenix.

> 2. The secondary structure definition in the PDB file header is not 
> recognizable anymore in Phenix.

Please send us an example and we will investigate!

> In my understanding, both the problems are arising due to PDB format's 
> inability to handle more than 62 chains and 99999 atoms in a file.

With two-letter chain id and hybrid36 (both are used in Phenix) this is 
not the case, you can have way more chains and atoms. And if you go to 
mmCIF (which is the standard, and also supported in Phenix), then these 
limitations are nonexistent.

Let us know if you have any questions or need help!


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