VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 21 2011 - 06:53:28 CDT

I think three atoms are not enough for a fit. Maybe using fictitious atoms is a sufficient solution, although I would add one additional atom for each of the three (so six in total) to properly weight it.

 Also, VMD uses the indices to pair atoms in a fit, meaning that C4 - C5 - C6 would be made to match with CAT-CBA-CAU, as you have found. To circumvent this, you need to use the flag "order" with the measure fit command. I believe this is documented in the VMD manual.
 
On Oct 20, 2011, at 6:25 AM, bio lab wrote:

> I am having trouble performing a very simple task in VMD: superimposing two molecules (hereafter called Label-capric and Capric) so that three atoms of the first molecule (called CAU CBA CAT) will correspond with three atoms of the second molecule (called C4 C5 C6).
>
> Both molecules are given below as pdb files (the first one is a spin-labeled capric acid created with Prodrg, the second one is a capric acid in all-trans conformation). The script I am using to superimpose them is also given below, and run in TK console with the command "source script.txt".
>
> 1. The first problem I see is that the script reported below *does not* superimpose the two groups of three atoms. I know that I could not expect the two groups to be exactly clashing, but I cannot believe that it is not possible to having them closer than several angstroms apart. Both CAU CBA CAT and C4 C5 C6 atoms are not aligned (i.e., there is no linear dependence in their positions) and their geometry is very similar, so they should end up being almost coinciding. I suspect there is a bug somewhere in VMD in superimposing groups of three atoms each.
>
> 2. Applying again and again the *same* script does not give again the same result. The two molecules end up being in different reciprocal positions, and usually very far away from each other. This is clearly a bug, and probably a different manifestation of the bug above. One way to workaround it (I do it, and VMD could do it internally as well) is to add in Label-capric a fictitious atom XXX with the same position as CBA and in Capric a fictitious atom YYY with the same position as C5. So now the superposition will be among *four* atoms ("name CAU CBA CAT XXX" and "name C4 C5 C6 YYY") and will make the two groups coincide almost exactly. But this lead to the last bug...
>
> 3. After running the script the two groups coincide as a whole, but there is no *direct* correspondence among the atoms. In other words, what is obtained is *not* a superposition CAU<->C4, CBA<->C5, CAT<->C6 (and XXX<->YYY). Instead, what is obtained is CAU<->C6, CBA<->C5, CAT<->C4. There is no way for me to change it, even selecting the atoms in a different order ("name CAU CBA CAT XXX" and "name C6 C5 C4 YYY" gives the same result). So I think this is a second (or maybe third) bug, and I cannot workaround it in any way.
>
> Any suggestion? Thanks in advance for your attention.
>
>
>
>
> ----- Label-capric.pdb -----
> HETATM 9 CAN DRG 1 5.910 20.490 -9.640 1.00 20.00 C
> HETATM 10 CAO DRG 1 5.520 19.360 -10.610 1.00 20.00 C
> HETATM 11 CAP DRG 1 4.840 18.140 -9.950 1.00 20.00 C
> HETATM 12 CAQ DRG 1 3.410 18.340 -9.450 1.00 20.00 C
> HETATM 13 CAT DRG 1 2.400 18.610 -10.580 1.00 20.00 C
> HETATM 14 CBA DRG 1 0.930 18.760 -10.120 1.00 20.00 C
> HETATM 15 CAU DRG 1 0.440 17.420 -9.520 1.00 20.00 C
> HETATM 16 CAR DRG 1 -0.980 17.380 -8.950 1.00 20.00 C
> HETATM 17 CAS DRG 1 -2.040 17.070 -10.010 1.00 20.00 C
> HETATM 18 CAX DRG 1 -3.450 17.240 -9.440 1.00 20.00 C
> HETATM 19 OAF DRG 1 -4.020 16.210 -9.010 1.00 20.00 O
> HETATM 20 OAD DRG 1 -3.920 18.400 -9.440 1.00 20.00 O
> HETATM 21 OAW DRG 1 0.790 19.820 -9.130 1.00 20.00 O
> HETATM 22 CAV DRG 1 0.660 21.050 -9.890 1.00 20.00 C
> HETATM 23 CAZ DRG 1 -0.270 20.680 -11.030 1.00 20.00 C
> HETATM 24 CAB DRG 1 -1.730 20.860 -10.630 1.00 20.00 C
> HETATM 25 CAC DRG 1 0.070 21.540 -12.250 1.00 20.00 C
> HETATM 26 NAY DRG 1 0.110 19.260 -11.250 1.00 20.00 N
> HETATM 27 OAE DRG 1 -0.270 18.480 -12.380 1.00 20.00 O
> -----
> ----- Capric.pdb -----
> HETATM 1 C1 STE 1 -10.027 1.729 0.294
> HETATM 2 O1 STE 1 -11.344 1.353 0.296
> HETATM 3 O2 STE 1 -9.683 3.095 0.360
> HETATM 4 C2 STE 1 -8.931 0.669 0.221
> HETATM 5 C3 STE 1 -7.565 1.348 0.234
> HETATM 6 C4 STE 1 -6.469 0.288 0.160
> HETATM 7 C5 STE 1 -5.103 0.967 0.174
> HETATM 8 C6 STE 1 -4.007 -0.092 0.100
> HETATM 9 C7 STE 1 -2.641 0.587 0.114
> HETATM 10 C8 STE 1 -1.545 -0.473 0.040
> HETATM 11 C9 STE 1 -0.179 0.206 0.053
> HETATM 12 C10 STE 1 0.917 -0.854 -0.020
> -----
> ----- script.txt -----
> set atomsel0 [atomselect 0 "name CAU CBA CAT"]
> set atomsel1 [atomselect 1 "name C4 C5 C6"]
> set M1 [measure fit $atomsel1 $atomsel0]
> set move1 [atomselect 1 "all"]
> $move1 move $M1
> -----
>