[phenixbb] Problems displaying disulphide links

Aaron Oakley aarono at uow.edu.au
Mon Apr 20 17:53:10 PDT 2020

How far apart are the SG atoms?

Do you have SSBOND records in your PDB file?


On 21 Apr 2020, at 3:33 am, Urvashi Sharma <urvashi.sha at gmail.com<mailto:urvashi.sha at gmail.com>> wrote:

Dear all,

I have a problems displaying disulphide links in PyMoL and CCP4mg for a 2.3 angstrom crystal structure. I have tried both PyMoL and CCP4mg, these programs are not recognizing an important inter-domain disulphide bridge which seems to have no problems in "Coot". While other intra-domain disulphide links are fine. Can anyone suggest how to manually fix it?

In addition, I have performed protein-protein docking using this crystal structure and have obtained nice convincing model. However, in this pose, which is being refined and energy minimized, none of the disulphide links are intact! Upon manual examination, I have noticed that the corresponding cysteine are 3.0-4.0 angstrom away. How should I correct this?

Looking forward to your suggestions...

With thanks and regards,


Dr Urvashi Sharma,
DBT-Ramalingaswamy faculty fellow
JNU, New Delhi.

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