My current files for modeller 9.14 (Mod9.14) were all in notepad, except for protein sequences in pdb format. I dont know how to change my files to .ali and .py format. Any suggestion?
Is this a problem? If you have a python script in a notepad (e.g. *.txt) file, then you can just save it as a *.py file. Otherwise you can rename the file in Explorer (changing *.txt to *.py).
Different formats of MSA files can be easily converted with online-services (such as MView: http://www.ebi.ac.uk/Tools/msa/mview/) or standalone software.
It's strange to see that your sequence files are in *.pdb format instead of *.seq, usually used by MODELLER.
If I didn't get you question right - please let me know and I'll try to do my best to help.
Best regards.
read this. make your basics clear. hope this will help you
http://salilab.org/modeller/tutorial/basic.html
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