Hi, The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close? Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992
Hi Abhinav,
The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close?
Possibly. Though we pick waters into Fourier maps (which are different from exact electron density distribution due to finite number of Fourier coefficients = finite resolution) so the peaks may be shifted. The smaller threshold distance is meant to account for this. As a side effect it increases the risk of interpreting bad pick. How big this risk (given all other peak selection criteria) - that I don't know: can take a few days to investigate. Also, it's a parameter - you can change it to match your taste.
Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density?
Currently not, but would be good to have, I agree. Pavel
Thanks Pavel. Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 08/01/2012 12:50 PM, Pavel Afonine wrote:
Hi Abhinav,
The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close? Possibly. Though we pick waters into Fourier maps (which are different from exact electron density distribution due to finite number of Fourier coefficients = finite resolution) so the peaks may be shifted. The smaller threshold distance is meant to account for this. As a side effect it increases the risk of interpreting bad pick. How big this risk (given all other peak selection criteria) - that I don't know: can take a few days to investigate.
Also, it's a parameter - you can change it to match your taste.
Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? Currently not, but would be good to have, I agree.
Pavel
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But it is possible to place two waters in those locations and assign different altloc identifiers to each. Correct? Best, Wally
Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? Currently not, but would be good to have, I agree.
Pavel
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Walter R.P. Novak Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149
Yes, you can do that. In my reply I meant it can't be done automatically by phenix.refine. Pavel On 8/1/12 6:46 PM, Walter Novak wrote:
But it is possible to place two waters in those locations and assign different altloc identifiers to each. Correct?
Best, Wally
Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? Currently not, but would be good to have, I agree.
Pavel
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Walter R.P. Novak Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149
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participants (3)
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Abhinav Kumar -
Pavel Afonine -
Walter Novak