Re: [modeller_usage] SequenceMismatchError when adding missing residues in LoopModel()

To: Modeller Caretaker <>

Subject: Re: [modeller_usage] SequenceMismatchError when adding missing residues in LoopModel()

From: Steven Truong <>

Date: Tue, 6 Apr 2021 01:12:13 +0000

Accept-language: en-US

Arc-authentication-results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=cam.ac.uk; dmarc=pass action=none header.from=cam.ac.uk; dkim=pass header.d=cam.ac.uk; arc=none

Arc-message-signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=x4BQUXZXfUBIU80t/W4tuNhgHhKhvrYNqxLkPD/PFX8=; b=Jpka19IyxSL5SesMpnYtSq9HsY4OFpAXXxhuweN6wJPT5lI2H28WDngkAdMx2g1p16gU/2wGNoEbNHXdfn8IS9FGyUoOTn0fMCgldH4NJ5pEE9x2fm1gCY9+LepNX+p2dUBKA2xqfM118VcpyAazceeXKkjnNlsLuhPTKNZlZDIZNDnE+DFbvI1FhDCk+0CMDq3ezrt/9wsfZPlhxcbK5yCp1Jyvu16H4+s75MTIPf1dhkvLEIOr5zjWxK7IRkXT02W7qCn7+EWdseeoZl93JdREvxNX71+SR7609qLQqMNY95IyznaVUYp7e8blucsXiIMdmkvzrQKEHXMAXbU8Yw==

Arc-seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=E7jxSX0WHxclu1KsSALVAKj/CqHi/x3UTjN1cB04KRMtq5E/laSR6fc7UxBd7MBC5z/nKikWLz+VkxjcU25wyJsx6CZCU5tbXnbZrpR3dHRcF6mlg0oc2RSiTIcVFamfnFUQzlzW+TnR7kFCbeIJXHNlKAmi64dRK2S0x6Zl2NsrOsa10xFGY6uxOK2szJ/qM0MLjzh0/Sp9GMglHeLMBS3WpS7YWOJqalvHPda+16wzZ6SMeZCBvIebANjluMBxbe0LRjl6TbNUkN2j6kaV7VIHSf/xhXbS1FatKXIBZQCqLYq5GGsLIxYPbLr8mCFVKd6pORUq/tYgrshQODFWxQ==

Cc: "" <>

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 <" class="">> 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
--
" class=""> https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage