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@n,ca,o,c #1:23@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@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@n,ca,c,o #1:23@n,ca,c,o
(hiding ribbon allows showing backbone atoms) You can also try selecting either set of atoms, for example:
select #0:346@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 that. 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@sib.swiss - http://www.sib.swiss