[phenixbb] help with pdbtools

Pavel Afonine pafonine at lbl.gov
Sat Mar 25 12:20:31 PDT 2017


Hi Ed,

it sounds like you want to get a bunch of shaken models. There is a 
better way of doing it by using dynamics which will stop at prescribed 
rmsd between starting and current models, also with a control that some 
bits of the model will not move too much.
Example:

1) Place all three attached files into an empty folder, and unzip pdb file.

2) Run

phenix.python run.py

You will get 10 PDB models each one different from each other and 
different from starting one by 0.5A.

You can edit run.py to add more models or increase difference.

3) Combine them all into one multi-model:

python run_combine.py

You will get all.pdb that looks like this: 
http://cci.lbl.gov/~afonine/tmp/pml.png

4) Get rid of junk:

rm -rf *log *geo

All files attached.

Let me know if you have any questions.

Pavel


On 3/25/17 11:38, Edward A. Berry wrote:
> Thanks Pavel, Oleg, that works now.
> I want the results to be different each time, so I guess I don't need 
> to do anything about the seed.
> I should have guessed about the spaces- I had no spaces in sites=0.5 
> and that part worked.
> Ed
>
>
> Oleg Sobolev wrote:
>> Hi Edward,
>>
>> phenix.pdbtools output.file_name=shake1.pdb 2chr_refine_001.pdb 
>> sites.shake=0.5
>>
>> should work to specify file name. Note that I removed spaces around =.
>>
>> As Pavel pointed out, results will be different.
>>
>> Best regards,
>> Oleg Sobolev.
>>
>>
>>
>> On Fri, Mar 24, 2017 at 11:17 PM, Edward A. Berry <BerryE at upstate.edu 
>> <mailto:BerryE at upstate.edu>> wrote:
>>
>>     1. I'm trying to use pdbtools and I don't quite get the syntax.
>>     How can I specify the output file name on the command line?
>>     these don't work:
>>     phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output 
>> file_name = shake1.pdb
>>     phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = 
>> shake1.pdb
>>     phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output 
>> file_name = shake1.pdb
>>     phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = 
>> shake1.pdb
>>     phenix.pdbtools --output file_name = shake1.pdb 
>> 2chr_refine_001.pdb sites.shake=0.5
>>     phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb 
>> sites.shake=0.5
>>
>>     2. for the "shake" operation, is there a random seed so that it 
>> comes out differently each time?
>>     (If I do this five times with different output file names, will 
>> they all be the different?)
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