[phenixbb] how to use a dimer as a search model by MRage

[Gabor Bunkoczi]

Dear Takaaki,

apologies, I have missed the point that you defined your search models 
as "templates" instead of "ensembles". If these are 100% identical 
models for the complex, then using an "ensemble" is the right thing to 
do.

You can use the phaser.MRage.solutions to extract solution N from the 
.pkl file:

phaser.MRage.solutions extract mrage_P61_results.pkl [--index=N]

However, it may be worthwhile to repeat the search with the dimers as 
search models, in case those give better solutions. Also, have you 
checked other space groups, such as P65?

Best wishes, Gabor


On 2014-12-09 01:15, fukamitka at chugai-pharm.co.jp wrote:
> Dear Gabor,
> 
> Thank you for your explanation how to specify dimers in a MRage input.
> I chose to use 'assembly' but got stuck. Please help me a little more.
> 
> 
> I added 'assembly { component { file_name = } }' sections as you wrote.
> This caused an error after alignment performed. Error message was 
> below:
> 
> 1. assembly:
>     1. component: dimerA-chain1.pdb
> Sorry: Cannot fine component: dimerA-chain1.pdb is not defined as an 
> ensemble
> 
> 
> Therefore I changed 'component { template { pdb = } }' sections to
> 'component { ensemble { coordinates { pdb = }} }', then it started to
> run. It ended with 19 partial solutions to a log file, and a result
> file  'mrage_P61_results.pkl', but no PDB file. I looked the result
> .pkl file, but it seems to be a dump of internal data from which I
> couldn't extract any information.
> 
> To obtain a structure of MR result, should I applied the partial
> solutions (4 EULER and FRAC value sets for 4 each subunit), or is
> there any option to write out the resultant structure?
> 
> Best regards,
> 
> Takaaki
> 
> 
> -----Original Message-----
> From: Gabor Bunkoczi [mailto:gb360 at cam.ac.uk]
> Sent: Friday, December 5, 2014 10:27 PM
> Subject: Re: [phenixbb] how to use a dimer as a search model by MRage
> 
> Dear Takaaki,
> 
> you have two options.
> 
> 1. If you do not expect the dimer structure to change, you can use
> them as one unit, i.e.:
> 
> composition {
>     component {
>       template {
>         pdb = dimerA.pdb
>       }
>     }
>     component {
>       template {
>         pdb = dimerB.pdb
>       }
>     }
> 
> In principle, you would need a sequence file for each dimer, in which
> the sequences are concatenated (instead of listed separately), but if
> this is not provided, MRage will calculate the molecular weight from
> the structure, and this is probably suitably close.
> 
> Perhaps the single-sequence check is slightly too conservative, and is
> primarily meant to catch common errors with sequence files. In light
> of your example, it may be better to interpret it that there are two
> sequences in the model.
> 
> 2. If you do expect some movement, you can specify assembly 
> information.
> In this case, your composition stays as it is, and you need tho add
> this to the PHIL:
> 
> assembly
> {
>      component
>      {
>          file_name = dimerA-chain1.pdb
>      }
> 
>      component
>      {
>          file_name = dimerA-chain2.pdb
>      }
> }
> 
> (and similarly for dimerB).
> 
> This tells MRage that once one component is located, the other one is
> possibly in the same relative orientation as dimerA-chain1.pdb and
> dimerA-chain2.pdb (if not, there are additional keywords to specify a
> transformation, primarily intended for homomultimers). There is also a
> "use_assembled" keyword that tells MRage to create an additional model
> of the dimer, but in this case, the monomer models are still present
> and used, and it is more efficient to run the dimer-only search as
> explained in 1.
> 
> Let me know if you need more help!
> 
> Best wishes, Gabor
> 
> 
> On 2014-12-05 12:36, fukamitka at chugai-pharm.co.jp wrote:
>> Dear all,
>> 
>> I have a dataset, there are 4 or 5 copies of two different hetero
>> dimers (i.e. 4 different chains) in au, and I'd like to use the dimers
>> as search models.
>> 
>> I ran phenix.MRage with a phil file below, and it searched each chains
>> separately, as expected. In this case, I want to search dimerA
>> (containing
>> chain1 and 2) and dimerB (chain3 and 4) as 2 search templates, but I
>> couldn't find how to specify a dimer as a component.
>> 
>> Using dimer.pdb and dimer.seq caused an error (sequence file can't
>> contain multiple sequence).  How do I write an input file?
>> 
>> Regards,
>> 
>> -------------------------
>> composition {
>>   count = 5
>>   component {
>>     sequence = dimerA-chain1.seq
>>     stoichiometry = 1
>>     template {
>>       pdb = dimerA-chain1.pdb
>>     }
>>   }
>>   component {
>>     sequence = dimerA-chain2.seq
>>     stoichiometry = 1
>>     template {
>>       pdb = dimerA-chain2.pdb
>>     }
>>   }
>>   component {
>>     sequence = dimerB-chain3.seq
>>     stoichiometry = 1
>>     template {
>>       pdb = dimerB-chain3.pdb
>>     }
>>   }
>>   component {
>>     sequence = dimerB-chain4.seq
>>     stoichiometry = 1
>>     template {
>>       pdb = dimerB-chain4.pdb
>>     }
>>   }
>> }
>> -------------------------
>> 
>> -----
>> Takaaki Fukami (mailto:fukamitka at chugai-pharm.co.jp)
>> Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical
>> Co.,Ltd.
>> 
>> 
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