Dear Ben,
I was hoping to follow up with a related question. Thank you for your help in the previous issue; I’ve been able to make it work finally.
If I have multiple structure templates, how would I tell when AutoModel should use which template? I see in the documentation (https://salilab.org/modeller/manual/node21.html) that you can build structures using AutoModel with multiple templates, but is there a way to specify which missing residues to fill in the alignment file? For example, can I use template1.pdb for all residues, except resid 50-60 and 100-130, and then use template2.pdb for resid 50-60 and 100-130?
Thank you for your help again! Steven Truong
On Apr 5, 2021, at 8:12 PM, Steven Truong <sdt45@cam.ac.ukmailto:sdt45@cam.ac.uk> wrote:
Dear Ben,
Okay, I think I see where I’m making the mistake then! Currently, I am following the tutorial (), and my interpretation was that “1qg8_fill” would be the template. It seems like that is NOT the case. Instead, we can ignore 1qg8_fill for our current purposes.
>P1;1qg8 structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00 PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------- -----EFVRNLPPQRNCRELRESLKKLGMG* >P1;1qg8_fill sequence::::::::: PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF ELEKNEFVRNLPPQRNCRELRESLKKLGMG*
I mistook the above and created a “6z43” template myself which contained the dashes like in 1qg8 in the tutorial. I’ll replace the dashes in that case with actual residues then. Thank you for the help!
Many thanks, Steven Truong
On Apr 5, 2021, at 8:02 PM, Modeller Caretaker <modeller-care@salilab.orgmailto:modeller-care@salilab.org> wrote:
On 4/5/21 5:42 PM, Steven Truong wrote: I think I have the template sequence alignment matching exactly to the PDB file, in the same way the second entry “1qg8_fill” has a full sequence. However, I am indicating missing residues with “1qg8.” Should I fill in those dashes with missing residues? I’m likely misunderstanding how AutoModel/LoopModel works then. When you refer to “template sequence,” is that “1qg8” or “1qg8_fill” in the align.pir file on the tutorial?
The template is the known structure, i.e. the PDB file, 1qg8 in the example.
>P1;6z43 structureM:6z43:27:A:+3600:C:::-1.00:-1.00 AYTNSFTR*-*VYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH--------------NPVLPF NDGVYFAST
Well, this simply isn't correct. The "missing" glycine here isn't missing in the 6z43 PDB file - it is there (residue 35 in chain A). What are you trying to accomplish here?
Ben Webb, Modeller Caretaker -- modeller-care@salilab.orgmailto:modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage