[Chimera-users] query regarding docking by chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 21 10:25:17 PST 2018

	What Elaine says below is all accurate.  I would add that the ‘gzip’ message merely means that the ‘gzip’ executable cannot be found on your system (which is completely normal for Windows) and therefore files compressed with gzip will not be able to be opened by Chimera (not normally an issue on Windows).
	When you run DockPrep, part of that procedure is to determine partial charges for non-standard residues.  Residue 13L in your structure is a large residue (38 atoms) and furthermore is covalently bonded to a cysteine, which adds yet more atoms to it for the purposes of charge determination.  Such a calculation will take many minutes.  So, Chimera wasn’t ‘hung’; if you had waited long enough the calculation would have finished.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 21, 2018, at 9:47 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Dr Effendi,
> The message says some file is gzipped and cannot be read.  Is some input file of yours gzipped (name ending in .gz)?  
> However, aside from that issue, I don’t understand why you are using Dock Prep anyway.  If you just want to look at the waters and co-crystallized ligand that are already in the crystal structure, there is no reason to use Dock Prep.  Just display the water and any other atoms you want to look at, for example (menu):
> Select… Structure… solvent
> Actions… Atoms/Bonds… show
> Take a look at the “getting started” tutorial to learn how to use Chimera.
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> Also, Dock Prep does not do docking.  It only prepares the structure for calculations with other programs, and by default it removes all the waters.  However, Chimera does have an Autodock Vina interface that does some limited single-molecule docking using a web service:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Feb 20, 2018, at 12:17 PM, Juweria Shahrukh Effendi <javelightens at yahoo.com> wrote:
>> Dear Daron 
>> I am new to chimera, I want to check the conserved water molecules in my protein pdb and its reported co-crystalized ligand 
>> as i do the dock prep complete 
>> adding hydrogen, applying charge, 
>> and i complete the whole steps the chimera isnt able to execute attaching the pic of both windows 
>> can you please have a  look on it and guide me 
>> thanks 
>> With Regards
>> Dr Juweria Shahrukh Effendi
>> M.B:B.S, M.Phil Biochemistry,
>> PhD Scholar (Computational Drug Design unit)Molecular Medicine
>> Dr Panjwani Center for Molecular Medicine and Drug Research
>> International Center for Chemical and Biological Sciences (ICCBS).
>> Karachi
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