July 2021 - modeller_usage

can we keep track of the modeller optimization process
by Li Xue 29 Jul '21

29 Jul '21

Hello, Is it possible that we could track all the details of the modeller conjugate gradients optimization process? For example, ask modeller at each optimization step to output the PDB coordinates, modeller molpdf energy terms and so on? Best, Li

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Sequence alignment with missing residues
by He, Amy 26 Jul '21

26 Jul '21

Dear Modeller experts, My apologies for the multiple posts. I’m using Modeller to align sequences, find missing residues in pdb and then perform loop modeling for the missing regions. And I have a small issue with sequence alignment when there’re missing residues. Here’s my .ali file: >P1;6cqx_a_unmod structureX:6cqx_a_unmod:3:A:+532:A:::-1.00:-1.00 -REDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTL YPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNY RVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGE.AGAASVGMHLLSPPSRGLFHRAV LQSGAPNGPWATVGMGEARRRATQLAHLVGCPPGG---NDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVP VVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAE AVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEI EFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNE-----APQWPPYTAGAQQYVSLDLRPLEVRRGLRA QACAFWNRFLPKLLSA-* >P1;6cqx_A sequence::: :: :::-1.00:-1.00 GREDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTL YPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNY RVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGESAGAASVGMHLLSPPSRGLFHRAV LQSGAPNGPWATVGMGEARRRATQLAHLVGCPPGGTGGNDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVP VVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAE AVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEI EFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNEPRDPKAPQWPPYTAGAQQYVSLDLRPLEVRRGLRA QACAFWNRFLPKLLSAT* And here’re the alignment commands I’m using: e = Environ() aln = Alignment(e) aln.append(file='two_seq.seq', align_codes=('all')) aln.align(gap_penalties_1d=(-600, -400)) aln.write(file='two_seq.ali') quit() The first sequence is read from a pdb file, with some residues (“-”). And the second sequence is the full sequence. However, because of the peculiar pattern, the alignment is not correct in this region: GCPPGG---NDTEL (from the pdb file) PPGGTGGNDTEL (the full sequence) I checked the structure file and then I found that the alignment should be as follows: GCPP---GGNDTEL (from the pdb file) PPGGTGGNDTEL (the full sequence) Is there any way to avoid this type of “mismatch” in the sequence alignment? Thank you very much for your kind advice in advance. Massive Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu

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Modeller objective function in the modeling of missing residues
by He, Amy 26 Jul '21

26 Jul '21

Dear Modeller experts, I’m a new user of Modeller and I’m using the x86_64 type of executable on Linux platform. I wanted to model some loop regions which are the missing residues in PDB structure, and basically I follow the “Missing residues” tutorial from the modeler website: https://salilab.org/modeller/wiki/Missing%20residues I have two questions: 1. About the "Modeller objective function" as an output score for each model: Could you help me understand what exactly the function is for the modelling of the missing residues? Is it a score for just the modelled loop region, or does it include the pair potential between the loop and the existent structure? 1. About the “md_level” of the loop refinement in “a.loop.md_level = refine.<option>”: Comparing the “fast” and the “large_slow” options, the “fast” option gave me models with better (lower) values of the “Modeller objective function”. Is this normal for the modeling of missing residues? Should I rather choose the “fast” option not the “large_slow”? Thank you for your time and kind advice in advance! Thanks, Amy

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Refining part of a model using another structure as reference
by Rafael Lemos 02 Jul '21

02 Jul '21

Hi, I have two questions/problems: 1. I need some help refining part of a model using another structure as reference. I tried the 'model-segment.py' script (https://salilab.org/modeller/manual/node23.html) but I'm unable to add the second structure (.pdb) to be used as the reference for the atoms that will be refined. 2. Is there a way to generate a model using only parts of two different structures? Like some residues from 'model1', and some from 'model2'. They are highly different sequences, so I tried modelling with multiple templates and got bad results. Thanks in advance.

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