[Chimera-users] Hello

A Amiri atefeh_amiri23 at yahoo.com
Tue Jul 30 14:48:35 PDT 2013

Hello again and thank you for helping.
I exactly need the formation a covalent bond and because of that i used the Join Model option and although i studied the Building Structure part of manual i coudn't understand that how two atoms, that the bond should be formed between them, are selected.
Please guide me more.Thanks.

 From: Elaine Meng <meng at cgl.ucsf.edu>
To: A Amiri <atefeh_amiri23 at yahoo.com> 
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu> 
Sent: Tuesday, 30 July 2013, 10:22:22
Subject: Re: [Chimera-users] Hello


Join Models is for when you want to combine models AND make a covalent bond between them. 



As explained in the link above, to use Join Models you must select two atoms in different models, each bonded to at most one other atom, to indicate where the bond should be formed, and enter values as needed to specify the geometry of bond formation (see the link for details).  The Apply button won't be active until those things are done.  (You can also see the manual by clicking the Help button on the dialog.)

However, if you just want to combine models and don't care about making a bond, you should instead use the "copy/combine" function in the Model Panel.  Model Panel is in the menu under Favorites.  Then you would have to choose the two models in the left side of the Model Panel to make the copy/combine button on the right side available.  Or, you can use the "combine" command that has the same capabilities as the Model Panel function.



I hope this helps,



Elaine C. Meng, Ph.D. 

UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab

Department of Pharmaceutical Chemistry

University of California, San Francisco

On Jul 30, 2013, at 5:29 AM, A Amiri <atefeh_amiri23 at yahoo.com> wrote:

> Hello.

> I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model.

> I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can  activate it!

> please help me.

> thank you for your useful software.
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