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

...

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

2008/2/6, Paul Adams : 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.

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- 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. --

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb