[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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>






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