[Chimera-users] Question about selection...
Yasser Almeida Hernández
pedro.al at fenhi.uh.cu
Tue Aug 10 07:49:27 PDT 2010
Hi...
The problem is that I have hundreds of pdb files with this format:
four models (or less), where each one is an aminoacid and a single
atom. Mostly, the single atom is an heteroatom and i select it with
:/isHet, but sometimes this atom is a protein atom with the ATOM field
and then, the :/isHet selection doesn't work...
There is some tricky way to select this single atom types (ATOM),
according to the structure of the pdb file...???
Thanks
Quoting Elaine Meng <meng at cgl.ucsf.edu>:
> 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... ;)
>
>
--
Yasser Almeida Hernández, BSc
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana, Cuba
Phone: (537) 214-3178
almeida at cim.sld.cu
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