[Chimera-users] Selection of residues and superposition

Alessandra Gastaldello Alessandra.Gastaldello at sib.swiss
Wed Jun 29 07:43:38 PDT 2016

Il 2016-06-24 20:21 Elaine Meng ha scritto:
>> Thank you so much Elaine! Very helpfull explanation about how to use 
>> match!
>> Despite that, I have a problem with some match and selection.
>> For some protein when I type for example:
>> match #0:346 at n,ca,o,c #1:23 at n,ca,o,c
>> to match those atoms in position 346 and 23, chimera tells me that the 
>> number of atoms is not the same.
>> How this is possible?
>> Thank again.
>> --
>> Alessandra Gastaldello
> Hi Allessandra,
> You’re welcome!  You would have to check specifically, but some
> reasons for different or unexpected numbers of atoms are:
> (1) a model has multiple chains, so that if you just say residue 23,
> there might be residue 23 in chain A, residue 23 in chain B, … to
> avoid this, just specify the chain directly. You can see which chains
> you have by putting the mouse over the structure and it will be shown
> in the pop-up information. For residue 23 in chain A only:
> #1.23.A at n,ca,c,o
> (2) one or more of the atoms is missing from a structure
> (3) structure has alternate locations of atoms, e.g. two positions of
> the same atom.  If there were locations A and B, you could first
> delete all the “B” locations in all structures with:
> delete @.b
> (4) residue number is incorrect so it did not specify any atoms
> Some ways to check are by trying to display all those atoms, for 
> example:
> ~ribbon
> disp #0:346 at n,ca,c,o #1:23 at n,ca,c,o
> (hiding ribbon allows showing backbone atoms)
> You can also try selecting either set of atoms, for example:
> select #0:346 at n,ca,c,o
> … and then see how many atoms are selected, such as by clicking the
> green magnifying glass in the bottom right corner to open the
> Selection Inspector.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

Thank you again Elaine! Very very useful.
Unfortunately, I have another question.
I would like to define a plane using the coordinates of some atoms in a 
structure and then to calculate the coordinates of the atoms that 
"surround" that plane. I know there is the "define plane" function to do 
But how can I get the coordinates of all atoms around that plane?

Moreover I would like to compare that coordinates with the coordinates 
of other atoms in other structures calculated in the same way (defining 
a plane).
In summary, I would like to see the atom distribution around some atom 
positions in different structures and to compare it.
This means I would have to have a same "reference" plane for all atoms 
even if they are in different structures.

Can I consider the different planes defined in the different structures 
as identical planes?
I mean, is each of them as an "origin" plane, spatially identical to 
other calculated in the same way?
Can I compare the coordinates of all the atoms in the different 
structures ?
Or should I define a big unique plane specifying coordinates from all 
the structures and after calculate the distance of the atoms from that 
unique plane?

Thank you very much in advance!

Alessandra Gastaldello
SIB | Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet - 1211 Geneva 4
t: +41 22 379 50 50 - f: ...
Alessandra.Gastaldello at sib.swiss - http://www.sib.swiss

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