November 2023 - modeller_usage

[modeller] sequence mismatch error
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure. However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

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DNA atoms changed by modeller
by Pedro Guillem 06 Nov '23

06 Nov '23

Hello all, I have a PDB with a small protein-DNA complex... I induce a point mutation in the protein and then save the mutated PDB. The DNA molecule remains untouched. I noticed my original pdb defines the first base (adenine) with 18 atoms - but the output modeller builds 21 atoms. The first 3 atoms are added. I believe the original input is missing the phosphate group. But I want modeller to leave the DNA alone the way it is. Is there a way to set modeller to leave some chains untouched in the output? Thanks in advance Pedro *MODIFIED BY MODELLER* *A* *TOM 1 P DA B 1 11.378 26.105 39.925 1.00 0.00 PATOM 2 OP1 DA B 1 11.702 25.899 40.057 1.00 0.00 OATOM 3 OP2 DA B 1 12.983 26.076 41.112 1.00 0.00 O* ATOM 4 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 5 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C *ORIGINAL* CRYST1 45.400 56.200 130.800 90.00 90.00 90.00 C 2 2 21 ATOM 1 O5' DA B 1 12.613 25.783 40.890 1.00 27.98 O ATOM 2 C5' DA B 1 13.939 25.889 40.375 1.00 25.91 C ATOM 3 C4' DA B 1 14.898 24.947 41.083 1.00 26.90 C ATOM 4 O4' DA B 1 14.923 25.240 42.497 1.00 26.42 O ATOM 5 C3' DA B 1 14.466 23.490 40.907 1.00 27.31 C ATOM 6 O3' DA B 1 15.624 22.725 40.560 1.00 29.53 O ATOM 7 C2' DA B 1 13.955 23.125 42.294 1.00 25.13 C ATOM 8 C1' DA B 1 14.747 24.029 43.236 1.00 24.42 C ATOM 9 N9 DA B 1 14.020 24.367 44.474 1.00 21.51 N ATOM 10 C8 DA B 1 14.404 24.071 45.742 1.00 20.32 C ATOM 11 N7 DA B 1 13.590 24.502 46.649 1.00 21.20 N ATOM 12 C5 DA B 1 12.581 25.132 45.948 1.00 20.03 C ATOM 13 C6 DA B 1 11.424 25.786 46.361 1.00 20.34 C ATOM 14 N6 DA B 1 11.075 25.916 47.640 1.00 20.30 N ATOM 15 N1 DA B 1 10.641 26.293 45.396 1.00 21.27 N ATOM 16 C2 DA B 1 10.993 26.155 44.127 1.00 20.67 C ATOM 17 N3 DA B 1 12.054 25.563 43.615 1.00 21.50 N ATOM 18 C4 DA B 1 12.825 25.060 44.609 1.00 21.31 C

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Making a heterotetramer model, while one of the chain is built by using two template
by rpw641＠sund.ku.dk 03 Nov '23

03 Nov '23

Dear Modeller users As the Subject said, I want to make a heterotetramer model, and make one of the chains by using two template. I know how to make heterotetramer model or build a single chain with multitemplate. The problem is that I don't know how to combine these two in my case. Thank you in advance Best Zhucheng

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