Hello everybody,
I have a little problem when measuring distances between C-alphas of
residues belonging to different proteins.
I have 3 proteins loaded (each with just one model, so: 1.1, 2.1 and 3.1),
the first one is a native protein, and the other 2 are homology models for
this protein.
My objective is to measure the distance between a residue of the native
protein (let's say residue 46, chain A) and the same residue in the 2
models, at once.
If I do:
set measureAllModels ON; set measurementUnits angstroms; measure (1.1 and
46:A.ca) (not 1.1 and 46:A.ca)
I get the output:
measurementUnits = "angstroms"
[[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/2.1 #362, 9.81 Å]
As expected, it measures just between the native protein and the first model
(the first occurrence of the second atom expression). So I need to use "set
measureAllModels ON".
But if I do:
set measureAllModels ON; set measureAllModels ON; set measurementUnits
angstroms; measure (1.1 and 46:A.ca) (not 1.1 and 46:A.ca)
I get the output:
measureAllModels = true
measureAllModels = true
measurementUnits = "angstroms"
[[ASP]46:A.CA/1.1 #338, [SER]49:A.CA/1.1 #362, 9.27 Å]
[[ASP]42:A.OD2/2.1 #338, [ASP]46:A.CA/2.1 #362, 14.85 Å]
[[ASP]42:A.OD2/3.1 #338, [ASP]46:A.CA/3.1 #362, 11.89 Å]
But I expect an output like:
measureAllModels = true
measurementUnits = "angstroms"
[[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/2.1 #362, 9.81 Å]
[[ASP]46:A.CA/1.1 #338, [ASP]46:A.CA/3.1 #362, x.xx Å]
What am I doing wrong?? Where do these 49:A.CA/1.1, 42:A.OD2/2.1,
42:A.OD2/3.1 atoms come from if they do not meet the atom expression stated
above???
Thanks a lot for your help,
Daniel
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