Re: [Jmol-users] update on altLoc or alternate conformation

[Bob H. <ha...@st...>]

Jan wrote:

> Miguel wrote:
>
>>> So something like this (if you prefer to predefine things):
>>>
>>> set defaultAltLoc  1A 2B 3B 4C
>>> load "filename"
>>>     
>>
>>
>> Yes, something like that.
>>   
>
> No.
> AltLoc is most useful for comparing models, if only one model is 
> loaded this isn't possible. All conformations in the PDB file should 
> be accessible after file load.
>
I see the point completely. We can implement it as one model load. I 
don't think it's an unsurmountable problem.

> I guess if it would be possible to define the AltLoc models before 
> load e.g.
> set AltLocModels((1%A/1, 2%B/1, 3%B/1, 4%C/1), (1%B/1, 2%C/1, 3%C/1, 
> 4%A/1), (1%C/1, 2%A/1, 3%A/1, 4%B/1), (1%A/2, 2%B/2, 3%B/2, 4%C/2), 
> (1%B/2, 2%C/2, 3%C/2, 4%A/2), (1%C/2, 2%A/2, 3%A/2, 4%B/2))
> in most cases we would be satisfied if we could
> join all conformations %A from the first MODEL in to one model and all 
> conformations %B/1 in a second and so on.
> set AltLocModels(for MODEL do for AltLoc do makeModel)
> It is enough if we could address 1%A/1, 1%B/1 or 1%A/2 to render them 
> differently and switch the visibility as it is possible in RasMol. I 
> even don't need models, though they are convenient for switching 
> visibility.
>
> Users may be fascinated by misusing AltLoc to visualize point mutations.
>
>> Or, maybe
>>   set altLoc "ABBC"
>>
>>  
>>
>>> Heaven forbid that on top of that there are multiple models with
>>> multiple altlocs,
>>>     
>>
>>
>> You are right ... what a disaster it would be with multiple models.
>>   
>
> 1SKT
> 1xhj
>
>>  
>>
>>> Yes, I suspect this is the more flexible way to go. Then you would
>>>
>>> select altloc=A
>>>
>>> meaning always "locations with only the default or specifically A".
>>>
>>> That wouldn't be so bad.
>>>
>>> How are different "runs" specified?
>>>     
>>
>>
>> Individual atoms are tagged with an altLoc identifier ... space or 'A',
>> 'B', 'C', etc.
>>
>> Generally, all of the ' ' atoms are together, followed the 'A's, then 
>> the
>> 'B's.
>>
>> When the atoms switch back to ' ' then we have reached the end of a 
>> 'run'.
>>
>> Basically, the software would need to read through the file and 'guess'
>> what constitutes a 'run'.
>>
>> Jan can probably tell us the 'worst cases' in terms of number of runs 
>> in a
>> file and the maximum number of alternates within a run.
>>
>>   
>
> No, I'm sorry, I am badly connected at the moment for PDB analysis, 
> but I guess BCDE*3 ~ 12 AltLoc per residuum is the worst case, but 
> only for special surface positions.
> The misuse for displaying point mutations may produce up to 20 AltLoc 
> conformations.
>
> I don't like the "correct" combinatorial AltLoc to model 
> implementation and vote for an AltLoc run implementation simply 
> joining *all* *%A into one and all *%B into an other model, this will 
> give 12 models to be generated (worst case, the number of alpha chars, 
> if the PDB file author sorrowfully only joins coexisting conformations 
> by a single char).
> Regards, Jan
>
>
>
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