Re: [phenixbb] A few questions

6 Feb 2008

      I will start implementing constrained group occupancy refinement today. 
It may take a few days and hopefully it will be available in one of the 
next versions of phenix.refine.

Pavel.

Rife, Christopher L wrote:
...
Yes, we did the refinement originally in shelx, but wound up with lots of NPD atoms, which is why we're trying some other options. So far we haven't been able to adjust the parameters in shelx sufficiently to correct the problems.
Regards,
Chris
-----Original Message-----
From: [email protected] [mailto:[email protected]] On Behalf Of Schubert, Carsten [PRDUS]
Sent: Wednesday, February 06, 2008 9:30 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] A few questions
Hi Chris,
to my knowledge SHELX is the only programs available wich handles these situations correctly. Since you have very good resolution SHELX may be (arguably) the better choice at this point until Pavel is done with the implementation.
Cheers,
Carsten
...
-----Original Message-----
From: [email protected]
[mailto:[email protected]]On Behalf Of Rife,
Christopher L
Sent: Wednesday, February 06, 2008 12:15 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] A few questions
In that case, then the occ of alt conf's tends to refine to 
greater than 1:
ATOM    523 SE  AMSE A  32      23.654  11.792   6.216  0.56 
14.04          Se
ATOM    530 SE  BMSE A  32      23.570  12.284   6.796  0.46 
13.91          Se
And, if I use "group_occupancy" plus H's, then all the 
residues refined to an occ of 0.99!
ATOM     30  N   ILE A   3      29.050  25.113   4.183  0.99  
8.48           N
It's fairly confusing...
In the end it seemed that the best option was to not include 
any occupancy refinement...
Chris
-----Original Message-----
From: [email protected] 
[mailto:[email protected]] On Behalf Of Peter Zwart
Sent: Wednesday, February 06, 2008 9:02 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] A few questions
I guess what is needed is not individual occupancy refinement, but
'grouped' occupancy refinement:
http://www.phenix-online.org/documentation/refinement.htm#anch106
HTH
Peter
2008/2/6, Paul Adams :
...
Hi Pavel,
the occupancy should be the same for all of the atoms in an
alternate conformation (grouped occupancy refinement). I
doesn't make
...
chemical sense for bonded atoms to have different occupancies.
Cheers,
        Paul
On Feb 6, 2008, at 8:56 AM, Pavel Afonine wrote:
...
Hi Christopher,
thanks for your questions!
...
We are working on a refinement at 1.14A which was suffering from
lots of NPD atoms when refined anisotropically with
refmac5 and/or
...
...
...
shelx.
The implementation of anisotropic B-factors refinement in
phenix.refine
should never lead to non-positive definite ADP matrices or any
"instability" in refinement.
...
1. In our model we have a few solvent ligands, and these show up
in the log file as:
          Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1}
          Classifications: {'undetermined': 13, 'water': 437}
We've used a cif file for EDO with H's when needed, but still see
this message. Is this normal? What is unusual?
Yes, it is normal. In this context "unusual" means that
this is not
...
...
"usual amino acid, water, dna/rna fragment".
...
2. When choosing "indivdual_occupancies" for the refinement, all
the atoms within an alt-conf are refined to different
occupancies-
...
...
...
is this expected? It seems that all atoms in the A conf should
have the same value, and the occ of all atoms in the B
conf should
...
...
...
also be the same. Instead, we see this:
ATOM    232  CA AGLU A  28      26.163   7.163   4.422  0.77
6.73           C
ATOM    233  CB AGLU A  28      24.851   7.269   3.672  0.80
9.27           C
ATOM    234  CG AGLU A  28      24.978   6.767   2.259  0.66
12.91           C
ATOM    235  CD AGLU A  28      23.662   6.717   1.554  1.00
16.51           C
ATOM    236  OE1AGLU A  28      22.874   7.667   1.757  0.71
18.78           O
ATOM    237  OE2AGLU A  28      23.429   5.733   0.803  0.60
16.77           O
ATOM    240  CA BGLU A  28      26.140   7.156   4.424  0.23
6.33           C
ATOM    241  CB BGLU A  28      24.794   7.230   3.713  0.20
6.48           C
ATOM    242  CG BGLU A  28      24.877   6.766   2.280  0.34
6.55           C
ATOM    243  CD BGLU A  28      23.536   6.702   1.598  0.00
7.53           C
ATOM    244  OE1BGLU A  28      23.497   7.014   0.381  0.29
7.85           O
ATOM    245  OE2BGLU A  28      22.543   6.341   2.280  0.40
8.40           O
This is correct behavior and this is exactly what you
should expect
...
...
refining occupancies of atoms in alternative
conformations: the sum of
...
...
occupancies of conformation A and B must be one. So, in your
example above:
ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C
...
ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C
the total occupancy is: 0.77+0.23=1
Same for other atoms.
...
3. Adding hydrogens during anisotropic refinement results in the
Parvati server giving "Illegal Biso" errors for many of the
hydrogens.
The H atoms at normal resolutions (not subatomic resolution) are
treated
as a special case. For example (default behavior), they
ride on bonded
...
...
atoms during coordinates refinement (riding model,
distances X-H do
...
...
not
change), we refine one occupancy and isotropic B-factor per all H
atoms
in your molecule, etc. I don't know what exactly "Illegal Biso"
means in
Parvati server, but most likely you want to exclude H
atoms for this
...
...
analysis.
Just a suggestion: at resolution 1.4A you can try to change the
default
behavior for H refinement to this:
hydrogens {
    refine_adp = *one_b_per_residue one_b_per_molecule individual
    refine_occupancies = *one_q_per_residue one_q_per_molecule
individual
  }
Please let us know if you have any questions or problems!
Pavel.
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--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology
Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
--
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