Hi,
I would like to know how to select main chain atoms for superposition
Thanks
Carlos Sosa
SET ATOM_TYPES = 'MNCH'
Andras
> Carlos Sosa wrote: > > Hi, > > I would like to know how to select main chain atoms for superposition > > Thanks > > Carlos Sosa
Hi, I have already written to you about this problem I have two different problems 1. I got the error messege read_al_375E> Unknown residue type,position,sequence: 1 7
The alignment is with known residue types with no HETATM int the pdb. The pdb file exists in the ATOM FILE DIRECTORY. Moreover, i got this error messege from running modeller on multipal alignment ,but when i ran each of the single alignments seperately i got the output model with NO error.
Does modeller check for interactions between the structures in the multipal alignment ?
2. Some pdb files like pdb1bb9.ent have their sequence like this
ATOM 153 ND1AHIS 30 24.022 -2.877 3.838 0.75 21.59 N ATOM 154 ND1BHIS 30 24.759 -2.618 2.211 0.25 41.12 N ATOM 155 CD2AHIS 30 22.589 -1.675 5.037 0.75 17.33 C ATOM 156 CD2BHIS 30 26.438 -1.699 3.249 0.25 41.31 C ATOM 157 CE1AHIS 30 23.214 -3.720 4.472 0.75 22.03 C ATOM 158 CE1BHIS 30 25.847 -3.286 1.875 0.25 41.29 C ATOM 159 NE2AHIS 30 22.402 -3.021 5.222 0.75 25.04 N ATOM 160 NE2BHIS 30 26.885 -2.754 2.494 0.25 40.59
modeller does not give output on such templates.
Thank you, Iris.
Hello,
1. I suspect a trivial problem, some file/sequence naming mismatch etc. This error is not in connections with any checking among input sequnces in the alignment.. If you cannot find the problem please send me the whole example.
2. It looks the pdb file is providing alternative solutions for the same structure or segment. Unfortunately the alternatives indicated as A and B after the atom types, which results unrecognizable atom types. Possibly you need to correct the file not only for A or B but to remove the duplicates.
what happens here is that in the (probably) very high resolution structure you can see different and relatively well defined atom occupancies in the diffraction map and consequently all the alternatives are reported (typically two forms). As you can see in the 8. column, there are 0.75 and 0.25 occupancy values for the two form. You can circumvent this problem by considering e.g. only the A form which has a higher occupancy.
Andras
sasson iris wrote: > > Hi, > I have already written to you about this problem > I have two different problems > 1. > I got the error messege read_al_375E> Unknown residue type,position,sequence: 1 7 > > The alignment is with known residue types with no HETATM int the pdb. > The pdb file exists in the ATOM FILE DIRECTORY. > Moreover, i got this error messege from running modeller on multipal > alignment ,but when i ran each of the single alignments seperately > i got the output model with NO error. > > Does modeller check for interactions between the structures in > the multipal alignment ? > > > 2. Some pdb files like pdb1bb9.ent have their sequence like this > > ATOM 153 ND1AHIS 30 24.022 -2.877 3.838 0.75 21.59 N > ATOM 154 ND1BHIS 30 24.759 -2.618 2.211 0.25 41.12 N > ATOM 155 CD2AHIS 30 22.589 -1.675 5.037 0.75 17.33 C > ATOM 156 CD2BHIS 30 26.438 -1.699 3.249 0.25 41.31 C > ATOM 157 CE1AHIS 30 23.214 -3.720 4.472 0.75 22.03 C > ATOM 158 CE1BHIS 30 25.847 -3.286 1.875 0.25 41.29 C > ATOM 159 NE2AHIS 30 22.402 -3.021 5.222 0.75 25.04 N > ATOM 160 NE2BHIS 30 26.885 -2.754 2.494 0.25 40.59 > > modeller does not give output on such templates. > > Thank you, > Iris.
participants (3)
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Andras Fiser -
Carlos Sosa -
sasson iris