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itasser model comptability with ucsf chimera strucure minimization
Posted: Wed Jan 17, 2024 4:31 pm
by zbu@ccny.cuny.edu
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
Re: itasser model comptability with ucsf chimera strucure minimization
Posted: Sun Jan 21, 2024 2:38 am
by zcx@umich.edu
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.
Re: itasser model comptability with ucsf chimera strucure minimization
Posted: Wed Jun 04, 2025 4:25 am
by Rosalyarza
zbu@ccny.cuny.edu wrote: ↑Wed Jan 17, 2024 4:31 pm
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
I’ve found I-TASSER very effective for predicting disordered protein segments.