From: Sarder Arifuzzaman <arifpharmju@gmail.com>
Subject: Inquiry for new/re-registration license key_Arifuzzaman Sarder
Date: July 31, 2018 at 9:08:53 AM PDT

Hi
Greetings.
This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is  giving us only protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. 
Thank you very much in advance. I am looking forward for your response please.  
Sincerely
Arifuzzaman, Sarder
PhD research fellow
Chung-Ang University
Mobile: 010-2654-2606


HI Arifuzzamman Sarder,
(forwarding to the proper address for asking Chimera questions: chimera-users@cgl.ucsf.edu )

There is no reason it should not work as before. Chimera does not use a license key.

For example, in Chimera 1.13,  command:

open pubchem:12123
(- or -)
open smiles:C1CCNC1

…shows a small molecule in sticks, and command:

open 2gbp

… shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks.

If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons.  To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save.

The behavior I described is for the default, “smart initial display” true.  If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure.

If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is.  However, if it is a graphics problem of your computer, it is not something we can fix.

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco