Hi Helena,

from the symptoms you are describing I am guessing that your definition of alternate conformations is somehow not correct. How did you generate the alternate conformations, in COOT, by hand, or by some other means? In my hands I only see the problem of bumping residues out of density when the alternate conformations are ill defined.  

This example (not tested) should work. The alternate location indicator is in column 17 (http://www.ccp4.ac.uk/html/pdbformat.html)

1        10        20        30        40        50        60        70        80

|........|.........|.........|.........|.........|.........|.........|.........|

ATOM   2133  N  AARG B   5      -8.859  76.908 -23.554  0.50 62.53           N

ATOM   2134  CA AARG B   5      -7.595  77.592 -23.916  0.50 73.84           C

ATOM   2135  CB AARG B   5      -6.685  77.736 -22.691  0.50 68.34           C

ATOM   2136  CG AARG B   5      -7.156  78.775 -21.687  0.50 64.25           C

ATOM   2137  CD AARG B   5      -6.073  79.165 -20.698  0.00 65.04           C

ATOM   2138  NE AARG B   5      -6.494  80.270 -19.841  0.00 63.73           N

ATOM   2139  CZ AARG B   5      -5.692  80.907 -18.995  0.00 62.76           C

ATOM   2140  NH1AARG B   5      -4.419  80.552 -18.890  0.00 62.59           N

ATOM   2141  NH2AARG B   5      -6.161  81.902 -18.255  0.00 62.33           N

ATOM   2142  C  AARG B   5      -6.823  76.908 -25.061  0.50 90.43           C

ATOM   2143  O  AARG B   5      -6.316  77.579 -25.965  0.50 84.57           O

ATOM   2144  N  BARG B   5      -8.759  76.908 -23.554  0.50 62.53           N

ATOM   2145  CA BARG B   5      -7.495  77.592 -23.916  0.50 73.84           C

ATOM   2146  CB BARG B   5      -6.585  77.736 -22.691  0.50 68.34           C

ATOM   2147  CG BARG B   5      -7.124  78.675 -21.625  0.50 64.25           C

ATOM   2148  CD BARG B   5      -6.176  78.831 -20.450  0.50 65.04           C

ATOM   2149  NE BARG B   5      -6.742  79.680 -19.405  0.50 63.73           N

ATOM   2150  CZ BARG B   5      -6.175  79.889 -18.223  0.50 62.76           C

ATOM   2151  NH1BARG B   5      -5.018  79.312 -17.929  0.50 62.59           N

ATOM   2152  NH2BARG B   5      -6.761  80.679 -17.334  0.50 62.33           N

ATOM   2153  C  BARG B   5      -6.723  76.908 -25.061  0.50 90.43           C

ATOM   2154  O  BARG B   5      -6.216  77.579 -25.965  0.50 84.57           O

HTH

Carsten

From: [email protected] [mailto:[email protected]] On Behalf Of Helena Taberman
Sent: Monday, January 11, 2016 6:55 AM
To: [email protected]
Subject: [phenixbb] Additional conformations and partially occupied waters

Hi,

I’m trying to refine a structure determined to 1.6 Å resolution. There’s several residues with additional conformations and waters with partial occupancies stating that they would be there when the conformation of the residues allows it. When I try to refine these conformations and partially occupied waters together the refinement kicks the second conformations and water molecules out of their densities, since they are obviously too close to the other additional conformations of the residues or the following residues. What could I do? Should I somehow group them together or what?

Best regards,

Helena

Helena Taberman, Ph.D.

University of Eastern Finland
Department of Chemistry
Joensuu Campus
P.O. Box 111
FI-80101 Joensuu, FINLAND

Mobile: +358 50 337 2488