January 2010 - phenixbb - phenix-online.org

occupancy refinement default selections - bug or feature?
by Ed Pozharski 21 Jan '10

21 Jan '10

There is a ligand residue in the structure that have its occupancy set to 0.75. refine with default parameters apparently refines every atom individually, so in the end I have a strange situation where ligand atoms have different occupancies. Of course, regular alternate conformers in the protein part of the structure have single occupancy refined per residue. Interestingly, when I place altLoc identifier "A" in front of the residue name of the ligand, single occupancy value is refined (although there is no second conformation). It settles down near 0.7 (close to what I selected previously based on a traditional approach of eliminating difference density and roughly matching B-factors of hydrogen-bonded protein atoms with ligand), so apparently constraints (e.g. total occupancy for all the conformers) are not applied. Is this intentional behavior (I understand that groups can be defined in the input file but adding altLoc letter seems like a simple trick)? I think most people would initially expect that occupancy will not vary within a residue, so the default behavior may seem like a bug to some (the only situation I can think of where such variation is justified is to model radiation damage). -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

2 1

Dear everybody
by YuYong Tao 21 Jan '10

21 Jan '10

Dear everybody: I installed phenix-1.6, when i run 'phenix.solve', it showed as follows: ustc-lifescience:~> phenix.solve binary=/usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=399459600 /usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory and when i run 'phenix.resolve' ,it seems to be ok. So i donn't know what to do. Can you tell me? Best Wishes!

2 1

How do different sections of TLS groups affect refinment
by Bart, Aaron G 21 Jan '10

21 Jan '10

Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron

5 6

K(sol) and B(sol)
by J. Fleming 20 Jan '10

20 Jan '10

Hi, I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help! -Jon

4 3

twin refinement in phenix-1.5-2
by Kelly Daughtry 20 Jan '10

20 Jan '10

Hello all, I am wondering if anyone has run across this problem and knows how to fix it. I have a twinned dateset and I am using phenix.refine to refine the dataset. I have the full 1.5-2 installation. When I include the twin law (-k, -h, -l) in the refinement, I get this error: File "/usr/swr/phenix-1.5-2/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1651, in map_coefficients "m_gradient" AssertionError If I do not include the twin law, I do not get the error and the refinment continues as normal. When I downgraded to Phenix.1.4-3 (full install), And use the same twin law, I am able to run phenix.refine without an error. I have attached my definition file for phenix.1.5-2 amd the log file. Thanks in advance for any help you can provide, Kelly Daughtry ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

5 5

Reflection file conversion
by Nate Nicely 20 Jan '10

20 Jan '10

I use d*TREK to reduce my data and phenix.reflection_file_converter to import the data. I seem to have had a bit of trouble generating the free R flags. It seems that the cap for the max number of free R reflections takes precedence over the percentage, even when the percentage is given expressly on the command line. I find myself setting the cap artificially high on the command line so that a full 10% is set aside. I was taught to set aside 10% for the free R set, only going lower if setting aside the full 10% compromised completeness. I'm just wondering what is the rationale for the numeric cap? Am I making any error(s) with my methodology? Nate N

4 4

Re: [phenixbb] clash guarde failure phenix coot
by Pavel Afonine 20 Jan '10

20 Jan '10

Hi Georg, I think the refinement .log file should contain the lines like these below: Warning: very small nonbonded interaction distances. Nonbonded interactions: 12604 Sorted by model distance: nonbonded pdb=" CG ARG A 3 " pdb=" CG ARG A 4 " model vdw 0.000 3.840 nonbonded pdb=" NE ARG A 3 " pdb=" NE ARG A 4 " model vdw 0.000 3.200 which pinpoints you the offending atoms. Does this answer your question? Pavel. On 1/19/10 9:57 AM, Georg Mlynek wrote: > > Dear All, > > I´m refining a 2.1A with phenix 1.5-2 and get when I click on > automatically add hydrogens to model following error message: > refinement.pdb_interpretation.clash_guard.failure: Number of nonbonded > interaction distances < 0.5:391 > > I suppose that this comes, because coot mixes up the hydrogens. >

1 0

rigid body refinement problem
by Jianghai Zhu 19 Jan '10

19 Jan '10

Hi, I am using phenix.refine_dev_282 for a rigid body refinement. The output pdb file is exactly the same as the input model even though there are obviously some large movements. Here are some information from the log file. Information about total rigid body shift of selected groups: rotation (deg) translation (A) xyz total xyz total group 1: 0.051 -5.493 -1.073 5.60 0.55 -3.15 -1.35 3.47 group 2: 0.254 0.562 0.252 0.67 0.36 -3.99 0.87 4.10 group 3: 3.807 4.001 -2.262 5.92 -0.81 -3.17 1.06 3.44 group 4: 2.275 -4.215 1.909 5.12 -0.18 -2.95 -1.43 3.28 group 5: -1.902 -5.750 -3.206 6.81 -1.99 -4.44 0.27 4.88 group 6: -4.932 -3.939 -5.340 8.16 -0.18 -2.08 -0.25 2.11 group 7: -1.140 -0.769 -7.715 7.83 0.73 -2.91 0.04 3.00 group 8: 2.008 -1.858 -1.236 3.02 -1.10 -5.44 -0.82 5.61 But then the model didn't change at all. stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_rbr: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_adp: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 Is this a bug? -- Jianghai

2 2

difference density map
by 丁玮 19 Jan '10

19 Jan '10

4 3

Where is phenix.refine finding starting r values?
by Bart, Aaron G 19 Jan '10

19 Jan '10

Greetings, I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? Regards -Aaron

2 1