Dear Henrique Musseli Cezar ,

Maybe a very simple method would be the use of Avogadro (free software and cross-platform). You could open your file *.pdb and remove by hand the hydrogens you don't want. Molden can be used also (free also) but the installation is more delicate than Avogadro.

Otherwise you can just go into the cif file (open it in a text editor) and delete tose three ydrogens by hand.

Hi Fernando,

I guess that the carbon atom is on a special position whereas the hydrogen atoms are not. This is because (in Shelx) the hydrogens are allowed to rotate about the carbon atoms. There is a possibility of using an anchor atom to fix the hydrogens also on special positions which makes the methyl group ordered.

In JANA2006, this could be done. If the downloaded .cif file has the .hkl information then you could try re-refining it again using the anchor and use it for converting it to pdb.

Or else, you could manually compute the special positions for hydrogens.

best regards,

Somnath

Thank you all for your help.

For future reference (search engines), I solved the problem using Olex2, according to the tips in this post: https://groups.google.com/g/diffpy-users/c/KKiVFnF5s3I/m/e01UB1EAAQAJ

Basically, I generated the full unit cell then removed the extra Hs by hand. Finally, I saved both an XYZ and a PDB, but the PDB generated by Olex2 did not have P 1 1 symmetry, so I just converted the XYZ to PDB using atomsk, but using the lattice parameters from the Olex2's PDB.