models in a structure

[yrxin]

Hi Xiangjun,

I used v2.0 to analyze ar0062. This structure has two models and 3dna can only find base pairs of model 1. I found that the difference between the two models is the alternative location.
Model 1:
ATOM      1  O5*A  C A   1   .....

Model 2:
ATOM      1  O5*C  C A   1   .....

In the 'misc_3dna.par' file, there is a line related to alternative location: alt_list: A1. How can I change this line in order to find base pairs in model 2.

Thanks,

Yurong

[xiangjun]

Hi Yurong,

Structure ar0062 (1zev) is sort of special in its handling of alternative location in ATOM or HETATM records. It is a crystal structure, yet the PDB format follows NMR ensemble by having two set of MODEL ... ENDMOL pairs, one for each alternative location (A and C). Normally, the alternative location is within a single PDB structure entry.

By design, the basic parts in 3DNA (find_pair/analyze etc) handles only a single structure. Here it corresponds to the first model, which happens to have A as indicator of its alternative location. By default, 3DNA recognizes "A1 " (e.g., A, 1, or  space) as alternative location.

To process the 2nd model, do the following:

Code: [Select]

ex_str -nmr -2 1zev.pdb 1zev_modelC.pdb
# change 'misc_3dna.par': "alt_list: C"
find_pair 1zev_modelC.pdb stdout

HTH,

Xiang-Jun