[Chimera-users] chimera help...please...

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 23 14:26:15 PDT 2011

On Mar 23, 2011, at 2:32 AM, Amit Kumar wrote:

> Dear Pettersen,
> first of all I like to thanks you as i am getting always nice  
> graphics from chimera software and hope you still involve in  
> improving it to compete all over good structure visualizers....
> I am a frequent user of this visualizer and already cited in all my  
> papers internationally published. I am struggling in getting ...

I'm happy you've gotten good results with Chimera, and thanks for the  
citations -- they help us get our funding renewed!

> 1) user guide of UCSF Chimera in pdf version as whole

If you go to the Chimera home page and click on the "Documentation"  
link, there will be a list of links to various documentation.  One of  
those links will be for a PDF of the 1.5 version of the User's Guide.   
It's about 12.5 MB (828 pages).

The Chimera documentation was always designed to be hyperlinked web  
pages, so the PDF version is not as well organized or concise as it  
would be if the documentation was PDF-based.  I hope you know that the  
HTML User Guide is bundled with each Chimera download and therefore  
all the Help buttons in dialogs, the "help" command, and the various  
functions in the Help menu just access your local copy and don't go  
over the web.

> 2) if  i build structure - add atom in structure ----whether we can  
> plced the atom at my desired place or coordination...if yes  
> how...and whether i can dragg that atom specifically to some unique  
> place....how?

The atom gets placed in the center of the view, so if you can get the  
center of the view to be your desired location then you're set.   
Otherwise, you can use the "Movement Mouse Mode" tool (in the Movement  
tools category) to move the atom wherever you want it positioned.

> 3)whether we can allign the specific atom/residue and accordingly  
> whole molecule....how? Although i use match maker that allign whole  
> molecules but my specific residue miss out

Use the "match" command to match specific atoms/residues.  Open the  
command line (Favorites->Command Line) and type "help match" for  
details.  As an example if you wanted to match residue 14 in model 0  
with residue 20 in model 1 (and they were the same residue type with  
the same atom names) then "match #0:14 #1:20" will move model 0 so  
that its residue 14 will be superimposed on model 1's residue 20.

> 4)how i can allign heteroatom like in my case i am trying to allign  
> heme from different hemoglobin molecule with maximum efficiency...as  
> heme are chemically same for both molecule it should allign  
> perfectly and accordingly their globin (apoprotein) part...

Similarly, if the hemes have the same number of atoms and the same  
atom names then something like "match #0:HEM #1:HEM" would work (also  
assuming only one heme per model).  If the hemes have differing  
numbers of atoms or different atom names then you would have to use a  
more detailed match command where you actually specify the atom names  
so Chimera knows which atoms to pair up in the match.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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