Re: [ccp4bb] REMARK 280 in mmcif? (and thoughts about "% w/v")

2020-01-26 Thread Edward A. Berry 

On 01/26/2020 01:02 PM, benjamin bax wrote:





Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
to produce the crystal.
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_exptl_crystal_grow_comp.html 


loop_
_pdbx_exptl_crystal_grow_comp.crystal_id
_pdbx_exptl_crystal_grow_comp.sol_id
_pdbx_exptl_crystal_grow_comp.comp_id
_pdbx_exptl_crystal_grow_comp.comp_name
_pdbx_exptl_crystal_grow_comp.conc
_pdbx_exptl_crystal_grow_comp.conc_range
_pdbx_exptl_crystal_grow_comp.conc_units
4'protein' 1  'protein'   25..  'mg/ml'
4'protein' 2  'Tris HCl'  20..  'millimolar'
4'protein' 3  'NaCl'   0.2   .  'molar'
4'precipitant' 1  'PEG 4000'  12.5   .  'percent_weight_by_volume'
4'precipitant' 2  'MES'0.1   .  'molar'
pdbout copy remarks 280



One argument against PDBX_EXPTL_CRYSTAL_GROW_COM is that it perpetuates (at least in this example) the 
incorrect/deprecated use of "%w/v". This is a measure of the mass concentration of the component, 
exactly the same as g/L or mg/ml. There is no reason to use different units for the same measure for 
different components. The valid use of % is when all components will add up to 100%, which is not the case 
for %w/v. Sigma used to sell a 1 g/ml solution of TCA in water as "100% w/v TCA". I wonder, how 
many people thought 100% meant pure TCA? Wikipedia is not authoritative, but the logic of the following (from 
article on "Volume Fraction") is compelling:

Terminology
'"Percent concentration" does not refer to this quantity. This improper name persists, especially in elementary textbooks. In 
biology, the unit "%" is sometimes (incorrectly) used to denote mass concentration, also called "mass/volume 
percentage." A solution with 1 g of solute dissolved in a final volume of 100 mL of solution would be labeled as "1 %" or 
"1 % m/v" (mass/volume). This is incorrect because the unit "%" can only be used for dimensionless quantities. Instead, 
the concentration should simply be given in units of g/mL.'

We all know that a 1% w/v solution contains 1 g of the component in question, 
per 100 ml of solution. It does not mean that that component makes up 1% of the 
mass of the solution, or 1% of the volume. It does not give us any better 
intuition into the amount of the compound present than would 1 g/100 ml or 10 
g/L. In fact it interferes with intuition, if other components are given in 
mg/ml. In the example above, is the amount of PEG more or less than the amount 
of protein (by weight)? 12.5% peg is 125 mg/ml, so 5-fold excess over protein 
by weight. Suppose you are told that for  a general rule when dissolving 
biological membranes with low-CMC detergents, start off with 1:1 ratio of 
protein:detergent. You want to solubilize your protein at 15 g/L. What should 
the detergent concentration be? Also 15 g/l, but the stock bottle is labeled 
20% w/v. You either convert 15 g/L to 1.5% or convert 20% to 200 g/L before you 
can calculate the volume to add. Not very hard, but for what??

Happy Lunar New Year,
eab



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Re: [ccp4bb] REMARK 280 in mmcif?

2020-01-26 Thread John Berrisford 
HI Ben

In mmcif we use _exptl_crystal_grow.pdbx_details.
See
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_exptl_crystal_grow.pdbx_details.html


John


On 26 Jan 2020, 18:02 +, benjamin bax , wrote:
>
> In PDB files you could put all information about protein delivery buffer, 
> crystallisation conditions and cryo conditions in
> REMARK 280
>
> (and pull it through in refmac with keyword
> pdbout copy remarks 280
> )
>
> Where are you meant to put all the information about what could be in your 
> crystal in mmcif_pdbx?
>
> Thanks, Ben
>
> Web (below) does not seem to give any very clear answers and I could not work 
> it out from looking at half a dozen recent pdb entries.
> Data item below is used in zero depositions. ..
>
>
> Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
>                details about the components of the solutions that were 'mixed'
>                to produce the crystal.
>      
> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_exptl_crystal_grow_comp.html
>
> loop_
> _pdbx_exptl_crystal_grow_comp.crystal_id
> _pdbx_exptl_crystal_grow_comp.sol_id
> _pdbx_exptl_crystal_grow_comp.comp_id
> _pdbx_exptl_crystal_grow_comp.comp_name
> _pdbx_exptl_crystal_grow_comp.conc
> _pdbx_exptl_crystal_grow_comp.conc_range
> _pdbx_exptl_crystal_grow_comp.conc_units
> 4    'protein'     1  'protein'   25.    .  'mg/ml'
> 4    'protein'     2  'Tris HCl'  20.    .  'millimolar'
> 4    'protein'     3  'NaCl'       0.2   .  'molar'
> 4    'precipitant' 1  'PEG 4000'  12.5   .  'percent_weight_by_volume'
> 4    'precipitant' 2  'MES'        0.1   .  'molar'
> pdbout copy remarks 280
>
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[ccp4bb] REMARK 280 in mmcif?

2020-01-26 Thread benjamin bax 

In PDB files you could put all information about protein delivery buffer, 
crystallisation conditions and cryo conditions in
REMARK 280

(and pull it through in refmac with keyword
pdbout copy remarks 280
)

Where are you meant to put all the information about what could be in your 
crystal in mmcif_pdbx?

Thanks, Ben 

Web (below) does not seem to give any very clear answers and I could not work 
it out from looking at half a dozen recent pdb entries.
Data item below is used in zero depositions. .. 


Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
   details about the components of the solutions that were 'mixed'
   to produce the crystal.
   
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_exptl_crystal_grow_comp.html

loop_
_pdbx_exptl_crystal_grow_comp.crystal_id
_pdbx_exptl_crystal_grow_comp.sol_id
_pdbx_exptl_crystal_grow_comp.comp_id
_pdbx_exptl_crystal_grow_comp.comp_name
_pdbx_exptl_crystal_grow_comp.conc
_pdbx_exptl_crystal_grow_comp.conc_range
_pdbx_exptl_crystal_grow_comp.conc_units
4'protein' 1  'protein'   25..  'mg/ml'
4'protein' 2  'Tris HCl'  20..  'millimolar'
4'protein' 3  'NaCl'   0.2   .  'molar'
4'precipitant' 1  'PEG 4000'  12.5   .  'percent_weight_by_volume'
4'precipitant' 2  'MES'0.1   .  'molar'
pdbout copy remarks 280


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