[Chimera-users] Command Patch problem

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 30 10:52:06 PST 2013

Hi Mahad,
You can search the manual using the Chimera menu: Help... Search Documentation.   For example, if you search for "renumber" it will show there is a Renumber Residues tool, in menu under Tools... Structure Editing.  You can also see lists of all the Chimera tools and commands in the User's Guide (also available under the Help menu).

You could try minimization, but in my experience it is not very good for improving  protein structures if they are tangled up or contain large distortions such as from adding multiple long bonds.  That is one reason we added "join models," to make it easy to join peptides without generating such distortions.   It always depends on your specific application, however, so you could try minimization... just be sure to save your session or structures before that, in case it does not help or makes everything worse.

On Jan 30, 2013, at 8:47 AM, mahad iou muddei addò wrote:

> Everytime i'm getting closer to what i need and it's all thanks to you! i used the "Adjust Bonds" command (after i manually put the 2 proteins in the position i wanted and combine them in a single structure) because it maintains the structure of my two protein and only adds the bond. Instead using "Join Models" every chain was bonded indipendently and this results in a conformation that is non useful for my work because the various chains moved following the bond but non according to each other (sorry for my bad explanation). Now i'm searching a way to rename every residue of the new model in a sequential way (Example: sequence residues number before 300-351 aa renamed in 1-51 aa) but i don't  have the solution right now. There is a function with chimera? And if i use the function "Minimize Structure" it will change the bonds added and make them better?
> Regards
> Mahad
> 2013/1/29 Elaine Meng <meng at cgl.ucsf.edu>
> Not sure I understand the question.  You could just repeat the process as many times as you need to.  If you meant that you want to join multiple chains from one structure to multiple chains in another structure (for example, A from first structure to A in second structure, B from the same first structure to B in the same second structure, ...) I think you would have to first split the second structure to make each of its chains a separate model.
> For example, if the second structure is open as model 1, you could split it with the command:
> split #1
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
> Then, you could use Join Models several times to combine the chains of the second structure (which are now separate models) with the chains of the first structure.  After each join, you would need to select one atom from the new combined model and then one atom from the next chain of the second structure.
> Another way to add bonds is with the Adjust Bonds section of the same tool, but that only works on atoms that are already within the same model.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
> Elaine

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