No superimposed PDB

[TomDongmin]

Hi, I am very much interested in using this program in my project. I am trying to align 831 predicted structures, they are well analysed with sequence alignments in previous studies but I am having problems in aligning them with Caretta. The run finishes well without an error message, but I can't find superimposed PDB file but only cleaned_pdb and result_pdb, and the result_pdb is virtually identical to the cleaned_pdb. also, I see very high RMSD values and very low TM scores which is not the case if I align some of them in PyMOL. Could you please help me to find what I am missing? Thank you in advance!

[fjell-dev]

I think you need to open/input all of the files in the result_pdb folder at once in PyMOL (or other molecular visualization software). Then you can see how they are aligned.

[TomDongmin]

I am still puzzled with the results, the RMSD scores are around 2K and TM scores of 0.06-0.08, which does not make sense as the aligned structures are quite conserved, and the TM score from the mTM-align is around 0.8. What could be the reason for this difference?

[Ninjani]

This sounds like a bug. Could you give a small set of PDB/AFDB IDs so I can reproduce and debug?

[TomDongmin]

Right! Okay, please find a small sample set of PDBs in the attachment. I ran Caretta and mTM-align with this set and similar results (reasonable results with mTM, but not with Caretta) came back. Thank you. From: Jay ***@***.***> Sent: 01 May 2023 12:27 To: TurtleTools/caretta ***@***.***> Cc: Kim, Tom ***@***.***>; Author ***@***.***> Subject: Re: [TurtleTools/caretta] No superimposed PDB (Issue #23) This email from ***@***.******@***.***> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. This sounds like a bug. Could you give a small set of PDB/AFDB IDs so I can reproduce and debug? — Reply to this email directly, view it on GitHub<#23 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6DG4EJO5EUVEOBPFF3YW2DXD6MZDANCNFSM6AAAAAAVGZXXBI>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[TomDongmin]

Here is the file, thank you!
D1_sam.zip

[Ninjani]

Thanks! Will look into it asap

[akdel]

Hi @TomDongmin, I'm getting high tm-scores for the dataset (D1_sam.zip) - are you sure you used the github repo and not the pypi version? I think it's safest to install caretta by cloning the master branch and pip install .. We'll also try to update the pypi version soon.

Here are the results that I got if you want to compare:

• tm.txt

13
7D1U_D1.pdb 1.0000 0.9788 0.9933 0.9878 0.9787 0.9847 0.9937 0.9876 0.9787 0.9788 0.9906 0.9786 0.9877
028_Synechococcus_sp__CB0101_unrelaxed_rank_1_model_3.pdb 0.9788 1.0000 0.9839 0.9986 0.9852 0.9990 0.9848 0.9997 0.9854 0.9854 0.9540 0.9852 0.9997
011_Synechococcus_sp__PCC_7335_unrelaxed_rank_1_model_3.pdb 0.9933 0.9839 1.0000 0.9819 0.9984 0.9824 0.9544 0.9802 0.9986 0.9990 0.9974 0.9972 0.9814
078_Nostoc_sp__ATCC_43529_unrelaxed_rank_1_model_3.pdb 0.9878 0.9986 0.9819 1.0000 0.9724 0.9888 0.9867 0.9983 0.9730 0.9729 0.9486 0.9780 0.9985
227_Tychonema_bourrellyi_unrelaxed_rank_1_model_3.pdb 0.9787 0.9852 0.9984 0.9724 1.0000 0.9683 0.9758 0.9713 0.9989 0.9995 0.9580 0.9991 0.9745
931_Pseudanabaena_sp__PCC_6802_unrelaxed_rank_1_model_4.pdb 0.9847 0.9990 0.9824 0.9888 0.9683 1.0000 0.9749 0.9906 0.9689 0.9689 0.9277 0.9824 0.9901
005_Pleurocapsa_sp__CCALA_161_unrelaxed_rank_1_model_4.pdb 0.9937 0.9848 0.9544 0.9867 0.9758 0.9749 1.0000 0.9850 0.9770 0.9767 0.9775 0.9884 0.9872
146_Chroococcidiopsis_sp__CCAL_unrelaxed_rank_1_model_4.pdb 0.9876 0.9997 0.9802 0.9983 0.9713 0.9906 0.9850 1.0000 0.9694 0.9701 0.9361 0.9857 0.9988
971_Hapalosiphonaceae_816_Fisc_unrelaxed_rank_1_model_3.pdb 0.9787 0.9854 0.9986 0.9730 0.9989 0.9689 0.9770 0.9694 1.0000 0.9995 0.9576 0.9974 0.9737
824_Synechococcus_sp__PCC_7336_unrelaxed_rank_1_model_3.pdb 0.9788 0.9854 0.9990 0.9729 0.9995 0.9689 0.9767 0.9701 0.9995 1.0000 0.9577 0.9980 0.9740
013_Leptolyngbya__sp__JSC1_01_unrelaxed_rank_1_model_4.pdb 0.9906 0.9540 0.9974 0.9486 0.9580 0.9277 0.9775 0.9361 0.9576 0.9577 1.0000 0.9600 0.9487
809_Xenococcus_sp__PCC_7305_unrelaxed_rank_1_model_4.pdb 0.9786 0.9852 0.9972 0.9780 0.9991 0.9824 0.9884 0.9857 0.9974 0.9980 0.9600 1.0000 0.9794
024_Cyanothece_sp__UBA12306_unrelaxed_rank_1_model_3.pdb 0.9877 0.9997 0.9814 0.9985 0.9745 0.9901 0.9872 0.9988 0.9737 0.9740 0.9487 0.9794 1.0000

• rmsd.txt

13
7D1U_D1.pdb 0.0000 3.7936 5.3624 3.4725 3.6266 3.7515 3.9823 3.0221 3.9627 3.8504 3.8358 3.1237 3.5606
028_Synechococcus_sp__CB0101_unrelaxed_rank_1_model_3.pdb 3.7936 0.0000 9.1885 3.8294 3.6279 4.0852 6.9149 5.9572 2.7761 3.2360 3.6569 5.3447 3.8534
011_Synechococcus_sp__PCC_7335_unrelaxed_rank_1_model_3.pdb 5.3624 9.1885 0.0000 7.5282 10.1748 14.1562 12.5715 12.0190 10.2528 9.9125 6.7260 10.5168 9.1813
078_Nostoc_sp__ATCC_43529_unrelaxed_rank_1_model_3.pdb 3.4725 3.8294 7.5282 0.0000 4.8290 5.6724 5.4407 6.3955 4.2368 4.3931 4.1894 6.1690 4.1712
227_Tychonema_bourrellyi_unrelaxed_rank_1_model_3.pdb 3.6266 3.6279 10.1748 4.8290 0.0000 4.9303 8.3048 4.8063 3.3880 2.6340 5.4907 3.6858 2.4609
931_Pseudanabaena_sp__PCC_6802_unrelaxed_rank_1_model_4.pdb 3.7515 4.0852 14.1562 5.6724 4.9303 0.0000 9.6888 6.3368 4.1850 4.4369 3.6811 4.4321 5.1607
005_Pleurocapsa_sp__CCALA_161_unrelaxed_rank_1_model_4.pdb 3.9823 6.9149 12.5715 5.4407 8.3048 9.6888 0.0000 10.5912 8.0227 7.9018 5.2881 8.5215 7.3407
146_Chroococcidiopsis_sp__CCAL_unrelaxed_rank_1_model_4.pdb 3.0221 5.9572 12.0190 6.3955 4.8063 6.3368 10.5912 0.0000 5.8674 5.4230 4.3031 2.4560 3.7260
971_Hapalosiphonaceae_816_Fisc_unrelaxed_rank_1_model_3.pdb 3.9627 2.7761 10.2528 4.2368 3.3880 4.1850 8.0227 5.8674 0.0000 2.0699 6.0345 4.9197 3.7684
824_Synechococcus_sp__PCC_7336_unrelaxed_rank_1_model_3.pdb 3.8504 3.2360 9.9125 4.3931 2.6340 4.4369 7.9018 5.4230 2.0699 0.0000 5.7499 4.4958 3.4205
013_Leptolyngbya__sp__JSC1_01_unrelaxed_rank_1_model_4.pdb 3.8358 3.6569 6.7260 4.1894 5.4907 3.6811 5.2881 4.3031 6.0345 5.7499 0.0000 3.4711 4.2502
809_Xenococcus_sp__PCC_7305_unrelaxed_rank_1_model_4.pdb 3.1237 5.3447 10.5168 6.1690 3.6858 4.4321 8.5215 2.4560 4.9197 4.4958 3.4711 0.0000 3.6651
024_Cyanothece_sp__UBA12306_unrelaxed_rank_1_model_3.pdb 3.5606 3.8534 9.1813 4.1712 2.4609 5.1607 7.3407 3.7260 3.7684 3.4205 4.2502 3.6651 0.0000