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boscoh / pdbremix

analyse PDB files, run molecular-dynamics & analyse trajectories
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Problem with a PDB #10

Open fab-genty opened 6 years ago

fab-genty commented 6 years ago

Hello, I use your program to compute the RMSD between the two PDB, one is a standard PDB and the other one is from a minimized PDB from attract .So, I get an error

./bin/pdbrmsd 1j5p_A.pdb out_1mjf_A_1mjf_B_sol_1.pdb 1j5p_A.pdb: all residues containing containing CA atoms out_1mjf_A_1mjf_B_sol_1.pdb: all residues containing containing CA atoms Traceback (most recent call last): File "./bin/pdbrmsd", line 66, in pdb1, pdb2, segments1, segments2, atom_types, transform_pdb1) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 196, in rmsd_of_pdbs atom_types, transform_pdb1) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 162, in rmsd_of_soups rmsd, transform_1_to_2 = calc_rmsd_rot(crds1, crds2) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 84, in calc_rmsd_rot return numpy_svd_rmsd_rot(crds1, crds2) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 38, in numpy_svd_rmsd_rot assert(crds1.shape == crds2.shape) AssertionError Here is the file

out_1mjf_A_1mjf_B_sol_1.txt

boscoh commented 6 years ago

Hi,

The error "assert(crds1.shape == crds2.shape)" means the list of CA atoms are not equal between the PDB structure. You should check if this is the case.

Bosco

On Fri, Dec 8, 2017 at 11:59 PM, fab-genty notifications@github.com wrote:

Hello, I use your program to compute the RMSD between the two PDB, one is a standard PDB and the other one is from a minimized PDB from attract .So, I get an error

./bin/pdbrmsd 1j5p_A.pdb out_1mjf_A_1mjf_B_sol_1.pdb 1j5p_A.pdb: all residues containing containing CA atoms out_1mjf_A_1mjf_B_sol_1.pdb: all residues containing containing CA atoms Traceback (most recent call last): File "./bin/pdbrmsd", line 66, in pdb1, pdb2, segments1, segments2, atom_types, transform_pdb1) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/ local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 196, in rmsd_of_pdbs atom_types, transform_pdb1) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/ local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 162, in rmsd_of_soups rmsd, transform_1_to_2 = calc_rmsd_rot(crds1, crds2) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/ local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 84, in calc_rmsd_rot return numpy_svd_rmsd_rot(crds1, crds2) File "/home/fabien/Documents/2017_18_M2BI_cours/Meet_U/test/ local/lib/python2.7/site-packages/pdbremix-.-py2.7.egg/pdbremix/rmsd.py", line 38, in numpy_svd_rmsd_rot assert(crds1.shape == crds2.shape) AssertionError Here is the file

out_1mjf_A_1mjf_B_sol_1.txt https://github.com/boscoh/pdbremix/files/1542685/out_1mjf_A_1mjf_B_sol_1.txt

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