[phenixbb] Real space refinement of complete virus structure

#TOFAYEL AHMED# TOFAYEL001 at e.ntu.edu.sg
Tue Mar 13 03:05:28 PDT 2018

Dear all,

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 but faced following problems:

1. This merged file is unreadable in UCSF Chimera.

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

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. So, what will be the work-around to perform a real space refinement of the complete virus structure at once? Also, how to maintain secondary structure during such refinement?

Any help is highly appreciated.

Best regards,



Tofayel Ahmed

Graduate Student (PhD) | Lab-02n-01

School of Biological Sciences

Nanyang Technological University

60 Nanyang Drive, Singapore 637551

+65 8650.0473 |tofayel001 at e.ntu.edu.sg<mailto:tahmed.pcu at gmail.com>

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