itasser model comptability with ucsf chimera strucure minimization

[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

[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.

[polytrack]

I-TASSER sometimes produces PDB files that are not fully PDB compliant, which can cause errors in other software like Chimera. The solution is to use the PDBFixer (or PyMOL) tool to correct the format or normalize the PDB file. PolyTrack