I've sent another message with attached example but I've recieved that the
size of attached file is too big ( 250kb) and this message must be checked
by moderators.
James
2012/6/1 Abhinav Verma <[email protected]>
> can you give us the exact pdb/code so that we can reproduce the problem ?
>
> On Fri, Jun 1, 2012 at 11:16 AM, James Starlight
> <[email protected]>wrote:
>
>> Dear PyMol users!
>>
>>
>> I've tried to make 1 point mutation by means of pymol's mutagenesis
>> wizard and obtain partially broken pdb.
>>
>> In my caseI've changed 276 residue from Leu to Tyr. As the consequence
>> the resulted pdb consist of wrong atom order ( you can see it inthe below
>> where new mutaded tyr is mixed with the atoms of the firstr residue and
>> partly with the atoms of second residue of that protein ( met-2 and gly-3
>> in that pdb).
>>
>> ATOM 1 N MET 2 30.865 33.218 71.898 1.00
>> 0.00 N
>> ATOM 0 N TYR 276 36.846 30.673 29.037 1.00
>> 0.00 N
>> ATOM 2 H MET 2 30.860 32.973 70.919 1.00
>> 0.00 H
>> ATOM 1 CA TYR 276 38.223 31.049 28.728 1.00
>> 0.00 C
>> ATOM 3 CA MET 2 30.563 32.110 72.824 1.00
>> 0.00 C
>> ATOM 2 CB TYR 276 38.572 32.435 29.346 1.00
>> 0.00 C
>> ATOM 4 CB MET 2 29.075 32.007 73.159 1.00
>> 0.00 C
>> ATOM 3 CG TYR 276 38.566 32.527 30.876 1.00
>> 0.00 C
>> ATOM 5 CG MET 2 28.699 32.785 74.409 1.00
>> 0.00 C
>> ATOM 4 CD1 TYR 276 39.655 32.065 31.622 1.00
>> 0.00 C
>> ATOM 6 SD MET 2 27.037 32.348 75.030 1.00
>> 0.00 S
>> ATOM 5 CD2 TYR 276 37.467 33.087 31.534 1.00
>> 0.00 C
>> ATOM 7 CE MET 2 27.384 30.784 75.811 1.00
>> 0.00 C
>> ATOM 6 CE1 TYR 276 39.644 32.168 33.011 1.00
>> 0.00 C
>> ATOM 8 C MET 2 31.021 30.724 72.375 1.00
>> 0.00 C
>> ATOM 7 CE2 TYR 276 37.458 33.188 32.922 1.00
>> 0.00 C
>> ATOM 9 O MET 2 31.124 30.414 71.189 1.00
>> 0.00 O
>> ATOM 8 CZ TYR 276 38.547 32.729 33.660 1.00
>> 0.00 C
>> ATOM 10 N GLY 3 31.434 29.985 73.384 1.00
>> 0.00 N
>> ATOM 9 OH TYR 276 38.542 32.830 35.022 1.00
>> 0.00 O
>> ATOM 11 H GLY 3 31.957 30.390 74.138 1.00
>> 0.00 H
>> ATOM 10 C TYR 276 39.196 30.036 29.278 1.00
>> 0.00 C
>> ATOM 12 CA GLY 3 31.510 28.518 73.329 1.00
>> 0.00 C
>> ATOM 11 O TYR 276 40.317 29.796 28.774 1.00
>> 0.00 O
>>
>>
>>
>> As the result when I've tried to process this pdb via Gromacs I've
>> obtained incorrect atom numbering etc. How this error could be fixed ?
>>
>>
>>
>> Thanks,
>>
>> James
>>
>>
>>
>>
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>
>
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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