Dear All, I am trying to run " LigandFit " with the following hydrated magnesium hexahydrate cluster (without the hydrogens) pdb. "HETATM 7 MG MG6 A 1 -53.936 117.342 91.273 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.351 117.224 89.749 1.00128.62 A O HETATM 3 O2 MG6 A 1 -52.532 117.421 92.718 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.370 118.284 92.428 1.00127.74 A O HETATM 5 O4 MG6 A 1 -53.253 119.219 90.518 1.00128.43 A O HETATM 6 O5 MG6 A 1 -54.385 115.379 91.937 1.00127.84 A O HETATM 7 O6 MG6 A 1 -52.566 116.391 89.994 1.00128.62 A O "
LigandFit automatically runs the elbow and creates a new search pdb file with hydroges and while doing this, elbow totally screws up the original starting geometry of the Oxygen atoms within the cluster after
Hi Hasan, I can help with part of this...yes, you can run without any connectivity...if you turn off real-space refinement: refine_ligand=False I took your mg hexahydrate and ran it that way and it ran through ligandfit just fine. All the best, Tom T the addition of hydrogens.
"HETATM 1 MG MG6 A 1 -53.913 117.323 91.231 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.140 117.947 90.141 1.00128.62 A O HETATM 3 O2 MG6 A 1 -53.080 118.061 92.589 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.453 117.480 92.061 1.00127.74 A O HETATM 5 O4 MG6 A 1 -52.768 118.528 90.669 1.00128.43 A O HETATM 6 O5 MG6 A 1 -53.676 115.727 91.923 1.00127.84 A O HETATM 7 O6 MG6 A 1 -53.363 116.194 90.004 1.00128.62 A O HETATM 8 H11 MG6 A 1 -55.461 117.161 89.473 1.00128.62 A H HETATM 9 H21 MG6 A 1 -52.333 117.378 92.967 1.00127.25 A H HETATM 10 H31 MG6 A 1 -55.430 118.350 92.700 1.00127.74 A H HETATM 11 H41 MG6 A 1 -53.300 119.422 90.378 1.00128.43 A H HETATM 12 H51 MG6 A 1 -54.636 115.255 92.077 1.00127.84 A H HETATM 13 H61 MG6 A 1 -52.319 116.372 89.793 1.00128.62 A H "
Is it a bug or am I making something wrong? Does the search pdb HAVE TO be covalently linked? or can I search for a cluster?
Thanks.
-- Hasan DeMirci _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb