[Chimera-users] centroid trace problems

Eric Pettersen pett at cgl.ucsf.edu
Sun Jul 31 22:52:03 PDT 2011

Hi Francesco,
	In that case there are two things you can do.  One is to use the '&'  
operator to select the residue that is number 225 and named HIS, like  

	:his & :225

Or, if you select the residue somehow (say by selecting an atom with  
the mouse and then using up-arrow to select the residue) you could  
name the selection with:

	namesel his225

and after that you can use 'his225' in exactly the same way you were  
trying to use ':his:225' before.


On Jul 31, 2011, at 10:38 PM, Francesco Pietra wrote:

> Hi Elaine:
> I could not use the residue number. This is a patched couple psf/pdb,
> where the various parts are bound together to establish chemical bonds
> within the enzyme active center. The various groups maintain the
> original residue number, which means that there are various different
> residue with the same number, and this applies in particular to the
> residue of my interest..
> francesco
> On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
>> Hi Francesco,
>> I'm glad to hear you like the centroid feature!
>> If you want only a specific residue, use only the residue number.   
>> If you
>> use both the name and the number you will get all of the residues  
>> with the
>> name, PLUS all of the residues with the number.  For example, if  
>> there are
>> three histidines HIS 126,152, and 225,
>> :his:225
>> will specify all three histidines.  To specify only HIS 225, use
>> :225
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                     http://www.cgl.ucsf.edu/home/meng/index.html
>> On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote:
>>> hello:
>>> "centroid" works fine to me in getting the trace of a moving  
>>> molecule
>>> in and out of a protein, using command
>>> define centroid radius 0.2 color red :residuename
>>> when the residue is unique. In fact, the method has produced
>>> extraordinarily illustrative (I am using the words of the referee)  
>>> in
>>> a paper that will appear shortly on Chemistry & Biodiversity. Now I
>>> have three diatomic molecules, only one of which is made moving
>>> around. In this case
>>> define centroid radius 0.2 color red :residuename:residuenumber
>>> for the moving residue does not work. What happens is that "red  
>>> balls"
>>> for the specified residue are being accumulated at the place of  
>>> origin
>>> of the residue, while the residue is leaving the protein as a short
>>> bar, not a ball. Could that be fixed in the above command?
>>> thanks
>>> francesco pietra
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list