Zhanglab forum

Dear Zhanglab,

I have been using itasser to predict the structure of disordered segments in proteins. It is a program better than alphafold or any other programs! However the pdb files of the model generated by itasser cannot be used in ucsf chimera for structure minimization. Do you have any suggestions to solve the problem?



Thanks,

Zimei Bu

Your issue is caused by the inability of UCSF chimera to recognize the hydrogen atoms in the I-TASSER model. In fact, structure minimization runs without any issue if the hydrogen atoms are removed prior to loading the structure into UCSF chimera.

I am not familiar with how to remove hydrogens in UCSF chimera, but this can be achieved by PyMOL by:
"A" - "Hydrogens" - "Remove" in the main window, followed by "File" - "Export Molecule" in the menu.

zbu@ccny.cuny.edu wrote: ↑Thu Jan 18, 2024 12:31 am Dear Monkey Mart,

I have been using itasser to predict the structure of disordered segments in proteins. It is a program better than alphafold or any other programs! However the pdb files of the model generated by itasser cannot be used in ucsf chimera for structure minimization. Do you have any suggestions to solve the problem?



Thanks,

Zimei Bu

I’ve found I-TASSER very effective for predicting disordered protein segments.

What steps can I take to prepare the PDB files generated by I-TASSER for compatibility with UCSF Chimera, specifically regarding hydrogen atoms?