[phenixbb] LigandFit (distorted manesium hexahydrate cluster)
Thomas C. Terwilliger
terwilliger at lanl.gov
Tue Dec 28 13:54:36 PST 2010
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
>> 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
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
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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