I have created a PDB of butane with the two central carbons (C1--C2) aligned along x (also attached)
REMARK This PDB file is created by CS Chem3D REMARK COMPND butane3.pdb HETATM 1 C UNK 0 -0.769 0.000 0.000 C HETATM 2 C UNK 0 0.769 0.000 0.000 C HETATM 3 C UNK 0 -1.383 -0.728 1.203 C HETATM 4 C UNK 0 1.382 -0.741 1.196 C HETATM 5 H UNK 0 -1.127 1.059 0.007 H HETATM 6 H UNK 0 -1.142 -0.461 -0.945 H HETATM 7 H UNK 0 -1.001 -0.311 2.163 H HETATM 8 H UNK 0 1.128 -0.488 -0.940 H HETATM 9 H UNK 0 1.143 1.051 -0.017 H HETATM 10 H UNK 0 -2.493 -0.625 1.206 H HETATM 11 H UNK 0 -1.156 -1.818 1.183 H HETATM 12 H UNK 0 2.492 -0.792 1.105 H HETATM 13 H UNK 0 1.155 -0.230 2.158 H HETATM 14 H UNK 0 1.000 -1.787 1.259 H
END I load the file and select a contiguous CH2CH3 fragment load butane3.pdb select atomno=2, atomno=4, atomno=8, atomno=9, (atomno>=12 and atomno<=14) now I want to rotate just this fragment about the C1--C2 bond rotateselected molecular x 20as far as I can see, the result is not correct; the C1--C2 bond moves on a cone, rather than remaining fixed. I think that rotateselected is rotating about the frame x axis, despite the use of the keyword molecular.
I am using version 11.2.8 Is this a bug, or have I misunderstood what I should be doing? Many thanks for your help James Keeler James Keeler, Director of Teaching Department of Chemistry, University of Cambridge Lensfield Rd, Cambridge CB2 1EW Tel. (01223) 336428 Secretary (Henneli Greyling) 336480 FAX 336362 WWW: www-keeler.ch.cam.ac.uk and www-teach.ch.cam.ac.uk
butane3.pdb
Description: Protein Databank data
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