[modeller_usage] Problem with Flex-em fitting

[Sushree Tripathy <>]

Hi,

I am trying to use flex-em using modeller 9.15. It is working fine with files given in tutorial. But I have got a structure with 4 chains and a corresponding cubic density map. 

1. Now if I am using the rigid.txt file as 

#helix 

#chain A

4:A   11:A

Then I am getting the error: KeyError: 'No such residue: 4:A'

2. If I am using the rigid.txt as 

#helix

#chain A

4       11

then I am getting the error: if resnum[-1] == 'nr':

IndexError: list index out of range

3. If I a, using the rigid.txt as 

#helix

#chain A

4       11 nr

then I am getting the error: _modeller.ModellerError: select__690E> Atom index      25 is in multiple rigid bodies!

4.  If I a, using the rigid.txt as 

#helix

#chain A

4:A:11:A:

14:A:21:A:

then I am getting the error: 

 list.add(mdl.residue_range(resnum[i], resnum[i+1]))

IndexError: list index out of range

Please let me know what is the correct format of rigid.txt file for multiple chains.

One more thing is my PDB contains 4 chains. So where can I give rigid bodies to all of them. Is it the no of iterations in flex-em.py file ?

Any suggestion is welcome. Please help.

Thanks

Sushree.