Nevermind. I just created a new function reset_defaults() to rewrite self.set_defaults() in automodel and I can get it. Thanks for your help.

-----Original Message----- From: modeller_usage modeller_usage-bounces@salilab.org On Behalf Of modeller_usage-request@salilab.org Sent: Friday, August 7, 2020 6:47 PM To: modeller_usage@salilab.org Subject: modeller_usage Digest, Vol 19, Issue 52

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Today's Topics:

1. Re: Change ROOT_NAME for automodel.make() (Modeller Caretaker) 2. Re: Change ROOT_NAME for automodel.make() (Brian Wiley)

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Message: 1 Date: Fri, 7 Aug 2020 15:33:39 -0700 From: Modeller Caretaker modeller-care@salilab.org To: Brian Wiley bwiley4@jhu.edu, "modeller_usage@salilab.org" modeller_usage@salilab.org Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make() Message-ID: 9ffc2904-4103-32e6-3c62-a4f8fd11a4f7@salilab.org Content-Type: text/plain; charset=windows-1252; format=flowed

On 8/7/20 2:21 PM, Brian Wiley wrote: > a = automodel(env, > alnfile = 'TSC2_6ssh.ali', > knowns = ('6ssh'), > sequence = 'TSC2_HUMAN') > > a.make() # Here I want the prefix to be 'TSC2_6ssh' and not > 'TSC2_HUMAN' so all files and pdb file at end would be > TSC2_6ssh.B99990001.pdb

automodel is written under the assumption that files are named for the sequence. If you want to name the output PDB files differently, that's straightforward; just override get_model_filename() as per https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or...

If you want to name the other output files differently, there isn't currently a mechanism for that, but it would be easy enough to modify the Python code to do so.

Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or... Modeller mail list: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or...

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Message: 2 Date: Fri, 7 Aug 2020 22:47:13 +0000 From: Brian Wiley bwiley4@jhu.edu To: Modeller Caretaker modeller-care@salilab.org, "modeller_usage@salilab.org" modeller_usage@salilab.org Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make() Message-ID: BYAPR01MB3622652122731C17B45282EAEF490@BYAPR01MB3622.prod.exchangelabs.com

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Thanks,

I would like to change the root_name for all the output file. It's kind of silly there is not class root_name attribute in automodel. Then you could just name that. I am having trouble overriding the __init__ in automodel because it calls self.set_defaults().

Brian

-----Original Message----- From: Modeller Caretaker modeller-care@salilab.org Sent: Friday, August 7, 2020 6:34 PM To: Brian Wiley bwiley4@jhu.edu; modeller_usage@salilab.org Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make()

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On 8/7/20 2:21 PM, Brian Wiley wrote: > a = automodel(env, > alnfile = 'TSC2_6ssh.ali', > knowns = ('6ssh'), > sequence = 'TSC2_HUMAN') > > a.make() # Here I want the prefix to be 'TSC2_6ssh' and not > 'TSC2_HUMAN' so all files and pdb file at end would be > TSC2_6ssh.B99990001.pdb

automodel is written under the assumption that files are named for the sequence. If you want to name the output PDB files differently, that's straightforward; just override get_model_filename() as per https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or...

If you want to name the other output files differently, there isn't currently a mechanism for that, but it would be easy enough to modify the Python code to do so.

Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or... Modeller mail list: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.or...