Fwd: [modeller_usage] Python Modeller Script

[Ricardo Nicoluci <>]

Hi,

I thought that the script was woriking well but after running a while the modeller gives the following error:

IOError: openf5__225E> File does not exist:  file-not-found
pdbnam__217W> Filename for PDB code not found:  adsl.B99990001.pdb
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
openf5__224_> Open       11  OLD  SEQUENTIAL  file-not-found
openf5__225E> File does not exist:  file-not-found


I checked the variable env.io.atom_files_directory and it is set to './' ...what am I doing wrong !?
Any ideia !?

Thanks,

On 9/27/05, Modeller Caretaker <" target="_blank" _onclick_="return top.js.OpenExtLink(window,event,this)"> > wrote:

Ricardo Nicoluci wrote:
> Sorry, I really forgot to attach the script file.
> I was trying to put generate.transfer_xyz between quotations marks.
>
> Now, if someone could comment the script, I would appreciate...

You call a.make() twice, so you'll build all your models twice, which is
inefficient. Get rid of the first a.make() call.

a.loop.md_level is the same as a.md_level - i.e. you should remove the
quotes from ' refine.very_slow'.

You don't need to pass topology_model, parlib, or toplib in the
loopmodel() constructor, since these are the defaults.

        Ben Webb, Modeller Caretaker
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Ricardo de Paula Nicoluci
PhD Student
Medicinal Chemistry Laboratory
IFSC - University of Sao Paulo
Sao Carlos - SP - Brazil