[Chimera-users] Question about selection...
Elaine Meng
meng at cgl.ucsf.edu
Mon Aug 9 13:53:18 PDT 2010
Hi Yasser,
Not sure whether you want to select the atom only in one specific model, or in all of them at the same time, so I'll answer both questions.
To select all of them, command:
select :561 at oe1
To select in just one model, include the model number. For example, if the file is opened as 0, the models in it are 0.1, 0.2, 0.3 ... so your command would be something like
select #0.1:561 at oe1
These are examples of "hierarchical" atom selections, described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy>
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
On Aug 9, 2010, at 1:21 PM, Yasser Almeida Hernández wrote:
> Hi chimerians...
>
> I have this pdb file with some models...
>
> MODEL
> ATOM 1 N ARG 2 75 3.566 -4.680 2.408 1.00 27.73 N
> ATOM 2 CA ARG 2 75 3.319 -3.762 1.307 1.00 27.44 C
> ATOM 3 C ARG 2 75 4.363 -2.641 1.381 1.00 27.43 C
> ATOM 4 O ARG 2 75 4.900 -2.249 2.434 1.00 26.54 O
> ATOM 5 CB ARG 2 75 1.901 -3.115 1.361 1.00 29.76 C
> ATOM 6 CG ARG 2 75 0.685 -4.005 1.574 1.00 30.19 C
> ATOM 7 CD ARG 2 75 1.021 -5.453 1.347 1.00 32.01 C
> ATOM 8 NE ARG 2 75 1.567 -5.689 0.064 1.00 35.22 N
> ATOM 9 CZ ARG 2 75 2.123 -6.788 -0.467 1.00 37.99 C
> ATOM 10 NH1 ARG 2 75 2.301 -7.901 0.253 1.00 37.85 N
> ATOM 11 NH2 ARG 2 75 2.343 -6.799 -1.796 1.00 37.02 N
> TER
> ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O
> TER
> ENDMDL
> MODEL
> ATOM 1 N ARG B 75 3.153 -4.497 2.431 1.00 25.72 N
> ATOM 2 CA ARG B 75 2.895 -3.593 1.311 1.00 26.52 C
> ATOM 3 C ARG B 75 3.980 -2.519 1.148 1.00 26.28 C
> ATOM 4 O ARG B 75 4.530 -2.055 2.176 1.00 26.18 O
> ATOM 5 CB ARG B 75 1.566 -2.890 1.541 1.00 30.04 C
> ATOM 6 CG ARG B 75 0.249 -3.353 1.047 1.00 33.78 C
> ATOM 7 CD ARG B 75 -0.666 -3.815 2.137 1.00 37.95 C
> ATOM 8 NE ARG B 75 -0.707 -5.248 2.257 1.00 42.21 N
> ATOM 9 CZ ARG B 75 -0.886 -6.067 3.286 1.00 44.76 C
> ATOM 10 NH1 ARG B 75 -1.060 -5.717 4.569 1.00 44.33 N
> ATOM 11 NH2 ARG B 75 -0.888 -7.403 3.027 1.00 45.78 N
> TER
> ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O
> TER
> ENDMDL
> MODEL
> ATOM 1 N ARG H 75 2.710 -4.027 1.931 1.00 41.50 N
> ATOM 2 CA ARG H 75 2.475 -2.983 0.948 1.00 38.30 C
> ATOM 3 C ARG H 75 3.422 -1.785 1.027 1.00 39.34 C
> ATOM 4 O ARG H 75 3.907 -1.419 2.105 1.00 38.57 O
> ATOM 5 CB ARG H 75 1.022 -2.521 1.055 1.00 41.90 C
> ATOM 6 CG ARG H 75 0.718 -1.195 0.370 1.00 48.73 C
> ATOM 7 CD ARG H 75 -0.639 -0.637 0.779 1.00 50.05 C
> ATOM 8 NE ARG H 75 -1.742 -1.354 0.145 1.00 56.64 N
> ATOM 9 CZ ARG H 75 -2.422 -2.353 0.705 1.00 57.10 C
> ATOM 10 NH1 ARG H 75 -2.121 -2.773 1.928 0.00 56.09 N
> ATOM 11 NH2 ARG H 75 -3.413 -2.931 0.040 0.00 56.09 N
> TER
> ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O
> TER
> ENDMDL
> MODEL
> ATOM 1 N ARG K 75 2.718 -3.987 1.949 1.00 40.34 N
> ATOM 2 CA ARG K 75 2.510 -2.935 0.974 1.00 40.91 C
> ATOM 3 C ARG K 75 3.439 -1.730 1.052 1.00 41.44 C
> ATOM 4 O ARG K 75 3.779 -1.257 2.143 1.00 44.22 O
> ATOM 5 CB ARG K 75 1.045 -2.492 0.991 1.00 46.88 C
> ATOM 6 CG ARG K 75 0.759 -1.285 0.109 1.00 57.01 C
> ATOM 7 CD ARG K 75 -0.722 -0.981 -0.005 1.00 64.03 C
> ATOM 8 NE ARG K 75 -0.939 0.301 -0.673 1.00 70.73 N
> ATOM 9 CZ ARG K 75 -0.576 1.482 -0.173 1.00 75.39 C
> ATOM 10 NH1 ARG K 75 0.025 1.563 1.009 1.00 75.51 N
> ATOM 11 NH2 ARG K 75 -0.798 2.594 -0.862 1.00 77.70 N
> TER
> ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O
> TER
> ENDMDL
>
> How can i select the 1 OE1 GLU atom in each the model?
> Any hint...
>
> Thanks... ;)
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