Re: [ccp4bb] Sketcher and stereochemistry

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: coot and stereochemistry
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

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Subject: Re: ccp4 pdb format
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

Subject: Re: Sketcher and stereochemistry
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

Whatever you do it is good practice to do your first run of refinement as
Review Restraints"

Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list

Then run the job and you will get a list of violations of restraints
If your chirality ideal is -2 and the calculated value is +2 then think
whether you have built the ligand wrongly or whetherthe sign is wrongly
defined.

Eleanor

PS - you will also find the bad clashes ..

Garib Murshudov wrote:
> Chiralities in refmac dictionaries are local just like in smile
> strings. You can of course put atoms by their priorities then
> you will have correspondence to R/S assignments. However you do not
> have to do it.
> In many case I find it useful to put chirality 'both' and then refine
> against this dictionary. This way you can handle severla stereoisomers
> (configurations) with the same dictionary.
>
> Regards
> Garib
>
> On 20 Mar 2007, at 00:49, Vu Thai wrote:
>
>> thanks for the link. I had already seen it and was using it to assign my
>> chirality. I guess I should clarify my question. In sketcher, does one
>> input the highest priority neighbor first, then the second, and
>> finally the
>> third? The sketcher GUI has three columns list: B/3, F/4, & 1/5. Do
>> these
>> columns have any significance?
>>
>> Vu
>>
>> On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud
>>
>> wrote:
>>
>>> Garib has documentation on his website that I presume matches what is
>>> required by sketcher. It can be found at
>>>
>>> http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html
>>>
>>> (I did a Google of "ccp4 chiral" to find it.)
>>>
>>> Dale Tronrud
>>>
>>> Vu Thai wrote:
>>>> Hi All,
>>>>
>>>> I was wondering how to properly define the stereochemistry for a
>>>> new ligand
>>>> in sketcher. In the sketcher interface there are three columns
>>>> after the
>>>> stereochem sign option. I would assume that the order in which you
>>>> enter
>>>> the chiral neighbors would effect the sign that you choose for your
>>>> stereochemistry. Does any one know how sketcher reads these three
>>>> columns
>>>> to determine the stereochemsitry?
>>>>
>>>> Thanks in advance for your help.
>>>> Cheers,
>>>> Vu
>>
>>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: coot and stereochemistry
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20

Next message:
Subject: Re: ccp4 pdb format
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-20