Super-positioning Not Working Correctly

[Former user]

Hello all, I have been trying to use coordinate superposition to align around ~33 PDBs. I have first put them all in a list, and read them as individual pdbs. I have been having trouble aligning these pdbs with: pdbs <- pdbaln(pdbfiles, fit = TRUE, ncore=1)

To superposition these I have used:

superimposed PDBs are written into “rough_fit” directory

xyz <- fit.xyz( fixed = pdbs$xyz[1,], mobile = pdbs, fixed.inds = gaps$f.inds, mobile.inds = gaps$f.inds, outpath = "fitted", full.pdbs = TRUE) Please take a look at the outputted PDBs that I have linked in Dropbox to take a look at the rough fits. Also, please do not hesitate to let me know if there is another method to align these PDBs by structure. https://www.dropbox.com/sh/43cs5583zm0a5dh/AACPjWHv3vddqfvJdLF52-y1a?dl=0

[Mehmet Sen]

I superimposed all these structures using PyMol, and wrote them into a directory. Then pdbfiles <- list.files('fitted' ,pattern=".pdb", full.names=TRUE)
aln <- pdbaln(pdbfiles, fit = FALSE, ncore=1)
pdbs <- read.all(aln)

here, rmsd for most of them looks okey, but 712_cA and 3mt0 are skyrocketing. When clustering analysis based on the pairwise structural deviation, it looks very apparent. I am not sure why RMSD for these structures are showing so high ?

I checked also the core.

core <- core.find(pdbs)

core size 87 of 88  vol = 2715.168 

core size 86 of 88  vol = 2460.74 

core size 85 of 88  vol = 2158.081 

core size 84 of 88  vol = 1908.922 

core size 83 of 88  vol = 1690.908 

core size 82 of 88  vol = 1439.592 

core size 81 of 88  vol = 1201.641 

core size 80 of 88  vol = 1058.859 

core size 79 of 88  vol = 967.129 

core size 78 of 88  vol = 899.92 

core size 77 of 88  vol = 842.035 

core size 76 of 88  vol = 776.242 

core size 75 of 88  vol = 726.205 

core size 74 of 88  vol = 671.263 

core size 73 of 88  vol = 616.246 

core size 72 of 88  vol = 557.563 

core size 71 of 88  vol = 496.512 

core size 70 of 88  vol = 445.275 

core size 69 of 88  vol = 392.899 

core size 68 of 88  vol = 341.463 

core size 67 of 88  vol = 290.047 

core size 66 of 88  vol = 262.023 

core size 65 of 88  vol = 233.668 

core size 64 of 88  vol = 211.982 

core size 63 of 88  vol = 196.307 

core size 62 of 88  vol = 180.621 

core size 61 of 88  vol = 165.349 

core size 60 of 88  vol = 145.056 

core size 59 of 88  vol = 127.808 

core size 58 of 88  vol = 109.964 

core size 57 of 88  vol = 96.142 

core size 56 of 88  vol = 84.304 

core size 55 of 88  vol = 77.831 

core size 54 of 88  vol = 71.312 

core size 53 of 88  vol = 65.533 

core size 52 of 88  vol = 62.468 

core size 51 of 88  vol = 57.363 

core size 50 of 88  vol = 52.419 

core size 49 of 88  vol = 47.093 

core size 48 of 88  vol = 39.794 

core size 47 of 88  vol = 36.666 

core size 46 of 88  vol = 33.865 

core size 45 of 88  vol = 30.862 

core size 44 of 88  vol = 28.275 

core size 43 of 88  vol = 25.774 

core size 42 of 88  vol = 23.45 

core size 41 of 88  vol = 21.546 

core size 40 of 88  vol = 20.533 

core size 39 of 88  vol = 19.106 

core size 38 of 88  vol = 17.869 

core size 37 of 88  vol = 16.613 

core size 36 of 88  vol = 15.077 

core size 35 of 88  vol = 13.576 

core size 34 of 88  vol = 12.36 

core size 33 of 88  vol = 10.874 

core size 32 of 88  vol = 9.424 

core size 31 of 88  vol = 8.462 

core size 30 of 88  vol = 8.115 

core size 29 of 88  vol = 7.263 

core size 28 of 88  vol = 6.506 

core size 27 of 88  vol = 5.801 

core size 26 of 88  vol = 5.265 

core size 25 of 88  vol = 4.687 

core size 24 of 88  vol = 3.07 

core size 23 of 88  vol = 2.508 

core size 22 of 88  vol = 2.187 

core size 21 of 88  vol = 1.904 

core size 20 of 88  vol = 1.682 

core size 19 of 88  vol = 1.495 

core size 18 of 88  vol = 1.258 

core size 17 of 88  vol = 1.101 

core size 16 of 88  vol = 0.917 

core size 15 of 88  vol = 0.706 

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[Mehmet Sen]

When aligned with clustalO,

core <- core.find(pdbs)

core size 78 of 79  vol = 15716.08 

core size 77 of 79  vol = 15387.96 

core size 76 of 79  vol = 15026.25 

core size 75 of 79  vol = 14364.56 

core size 74 of 79  vol = 13515.16 

core size 73 of 79  vol = 12665.02 

core size 72 of 79  vol = 11875.1 

core size 71 of 79  vol = 11118.54 

core size 70 of 79  vol = 10362.6 

core size 69 of 79  vol = 9712.498 

core size 68 of 79  vol = 9148.719 

core size 67 of 79  vol = 8659.854 

core size 66 of 79  vol = 8220.31 

core size 65 of 79  vol = 7776.458 

core size 64 of 79  vol = 7292.426 

core size 63 of 79  vol = 6934.914 

core size 62 of 79  vol = 6590.951 

core size 61 of 79  vol = 6333.708 

core size 60 of 79  vol = 6037.72 

core size 59 of 79  vol = 5698.591 

core size 58 of 79  vol = 5318.235 

core size 57 of 79  vol = 5005.614 

core size 56 of 79  vol = 4673.907 

core size 55 of 79  vol = 4368.755 

core size 54 of 79  vol = 4120.801 

core size 53 of 79  vol = 3907.722 

core size 52 of 79  vol = 3685.601 

core size 51 of 79  vol = 3449.771 

core size 50 of 79  vol = 3257.606 

core size 49 of 79  vol = 3075.494 

core size 48 of 79  vol = 2899.273 

core size 47 of 79  vol = 2659.253 

core size 46 of 79  vol = 2545.403 

core size 45 of 79  vol = 2405.802 

core size 44 of 79  vol = 2257.884 

core size 43 of 79  vol = 2097.893 

core size 42 of 79  vol = 1879.069 

core size 41 of 79  vol = 1748.34 

core size 40 of 79  vol = 1634.665 

core size 39 of 79  vol = 1522.438 

core size 38 of 79  vol = 1414.559 

core size 37 of 79  vol = 1287.81 

core size 36 of 79  vol = 1182.517 

core size 35 of 79  vol = 1103.353 

core size 34 of 79  vol = 990.171 

core size 33 of 79  vol = 881.461 

core size 32 of 79  vol = 818.716 

core size 31 of 79  vol = 770.49 

core size 30 of 79  vol = 699.079 

core size 29 of 79  vol = 640.03 

core size 28 of 79  vol = 590.743 

core size 27 of 79  vol = 542.518 

core size 26 of 79  vol = 503.552 

core size 25 of 79  vol = 461.028 

core size 24 of 79  vol = 416.206 

core size 23 of 79  vol = 359.048 

core size 22 of 79  vol = 263.741 

core size 21 of 79  vol = 216.183 

core size 20 of 79  vol = 192.974 

core size 19 of 79  vol = 177.832 

core size 18 of 79  vol = 160.434 

core size 17 of 79  vol = 143.061 

core size 16 of 79  vol = 121.615 

core size 15 of 79  vol = 102.53

[Xinqiu Yao]

Hi,

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From your rought_fit directory I noticed that you didn’t separate chains. Are you sure it is what you want? Different PDB files may have different number of chains and sometimes different chains may represent completely different proteins! This may cause problems in the alignment and then the superimposition.

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[Mehmet Sen]

Hi Xinqiu,

Actually, all are single-chain proteins. Some are ~260-280 residue-long and some are 130-140 residue long, the latter is basically half of the former. The longer ones are monomeric, and shorter ones are dimeric. As you could see, they superimpose very well.

Cheers,

Mehmet

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