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Hello,
I am new to the imp-users mailing list.
I am having trouble running PMI. I am following the online RNA Polymerase example (http://integrativemodeling.org/2.5.0/doc/manual/rnapolii_stalk.html) and adapting it to suit my own protein complex.
When I run the modeling.py script, I seem to get as far as defining my x-links, then the program optimizes floppy bodies, lists all my proteins, then crashes.
The crash takes place with the following error;
(after x-linking information)
Generating a NEW crosslink restraint with an uniqueID 45 -------------- ISDCrossLinkMS: generating cross-link restraint between ISDCrossLinkMS: residue 89 of chain mol1d and residue 559 of chain mol2c ISDCrossLinkMS: with sigma1 1.000000 sigma2 1.000000 psi 0.05 ISDCrossLinkMS: between particles mol1d_89_pdb and mol2c_536-585_bead_floppy_body_rigid_body_member ==========================================
optimize_floppy_bodies: optimizing 49 floppy bodies mol2a_1 mol2a_2 mol2a_3 mol2a_4 mol1b_1 mol2c_1 mol2c_2 mol2c_3 mol2c_4 mol1d_1 mol3_1 mol3_2 mol4f mol4g mol4h mol4i mol4j mol4k mol4l mol4m will scale target mass by 454684.664 mass_scale=target_mass_scale) File "/usr/local/lib/IMP-python/IMP/isd/gmm_tools.py", line 29, in decorate_gmm_from_text weight=float(fields[2]) IndexError: list index out of range WARNING Object "linker_restraints" was never used. See the IMP::Object documentation for an explanation. Can anyone advise me what the issue here is? Does it relate to my target GMM file?
I am at a loss.
Yours,
Jason
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