Hello Maria Taj Muhammad,
The address for questions about using Chimera is chimera-users@cgl.ucsf.edu (CC’d here).

Chimera does not read chemdraw.cdx files, sorry.

Here is a list of the atomic-structure formats that Chimera can read:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct>

You would probably want to use PDB, Mol2, or (MOL) SDF for your ligands, to read them in to Chimera.  Then you can use the Dock Prep tool (in menu under Tools… Structure Editing) to add hydrogens and charges and save as Mol2.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 22, 2017, at 7:55 AM, Williams, Joanne <Joanne.Williams@ucsf.edu> wrote:
>
> From: bushra TAJ <bushraistaj@gmail.com>
> Date: Thursday, May 18, 2017 at 10:53 PM
> Subject: Re: chimera download

>
> Hello Sir
> will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format???
> What format I can take of my ligand to load in Chimera??
>
> On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj@gmail.com> wrote:
>> My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN.
>> is that OK
>> Regards
>>