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