[IMP-users] Help with validating IMP model, and also a topology file question

[Cecilia Sanders <>]

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• To: "imp-users@listsrv.ucsf.edu" <imp-users@listsrv.ucsf.edu>
• Subject: Help with validating IMP model, and also a topology file question
• From: Cecilia Sanders <>
• Date: Mon, 21 Sep 2026 16:59:42 +0000
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Hello, I have gotten my IMP modeling program to give me an integrated model of the CCT complex folding a 105-kDa substrate within its chamber in the open form, with the data inputs of a cryo-EM map and about 10 each of BS3 and EDC crosslinks: 

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Hello,

I have gotten my IMP modeling program to give me an integrated model of the CCT complex folding a 105-kDa substrate within its chamber in the open form, with the data inputs of a cryo-EM map and about 10 each of BS3 and EDC crosslinks: 

I am now struggling with two things:

1. The low ~5-angstrom resolution of the substrate in the cryo map suggests that is not completely folded, but the program is modeling it in its fully folded state and aligns almost completely with the PDB I referenced it to in the topology file. I am wondering if I could modify the topology file to allow for a lesser degree of folding and more flexibility in this substrate? Is it better not to reference it to a PDB of the fully folded substrate? And if so, how do I adjust the rigid_body|super_rigid_body|chain_of_super_rigid_bodies values to have the beads make sense? Below is my topology file entry for the substrate:

|molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|

|substrate|black|Nsp12_CCT.fasta|Nsp12_delta10_strep|BEADS||1,1|0|50|50||17||

|substrate|black|Nsp12_CCT.fasta|Nsp12_delta10_strep|Nsp12d10_7RDX_renumbered_CCT_8SFE_singlemodel.pdb|L|2,921|0|1|10|17|17||

|substrate|black|Nsp12_CCT.fasta|Nsp12_delta10_strep|BEADS||922,925|0|10|10|17|17||

|substrate|black|Nsp12_CCT.fasta|Nsp12_delta10_strep|BEADS||926,958|0|10|10||17||

2. Validation. The image above is the best that I've gotten from a 40k-frame run and included a total score that stopped decreasing at about 20k frames. However, subsequent identical runs have given clash, unstable scores, lack of crosslink distance optimization, and drastically different positions of the substrate (CCT is fixed). I run into similar problems by adjusting the slope of the EM restrain or the weights of the crosslinks, leaving me uncertain about weight adjustments. I read through your 121216_workshop_validation presentation but am still feeling uncertain of steps to proceed. I do have four other cryo maps from 3DVA that I could use for bootstrapping/jackkniifing, but am hesitant to cut down on the crosslink set since it is already sparse due to a stringent FDR.

Attached is my production script. Thank you so much for any guidance you're able to provide.

With appreciation,

Cecilia Sanders

6^th year Ph.D. student, Barry Willardson Lab

BYU Dept. of Chemistry and Biochemistry

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