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estimated coordinate error
by Jianghai Zhu 02 Aug '07

02 Aug '07

Hi, I am refining a 2.6 A structure using both phenix.refine and refmac5. Both programs give me similar R and Rfree values. But the estimated coordinate errors are quite different. From phenix.refine: maximum likelihood estimate for coordinate error: 0.42 A From refmac5: estimated overall coordinate error: ESU based on R value: 0.427 A ESU based on Free R value: 0.293 A ESU based on maximum likelihood: 0.239 A I am wondering why they are different. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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General Question !!!
by john kryst 01 Aug '07

01 Aug '07

Hi all !! Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement. regards John

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AutoSol problem
by Ben Eisenbraun 31 Jul '07

31 Jul '07

Hi- One of my users is running the Linux 64-bit version of Phenix-1.3b and they are getting the following message at the end of their logfile: ************************************************************ Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ************************************************************ The solve part of Phenix looks like it built correctly: $ ls -l phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/ -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment_pair -rwxr-xr-x 1 sbgrid sbgrid 3483160 Jun 27 16:55 resolve -rwxr-xr-x 1 sbgrid sbgrid 3483576 Jun 27 16:55 resolve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 3483256 Jun 27 16:55 resolve_giant -rwxr-xr-x 1 sbgrid sbgrid 3482968 Jun 27 16:55 resolve_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_giant -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_huge -rwxr-xr-x 1 sbgrid sbgrid 1547840 Jun 27 16:55 segment_library -rwxr-xr-x 1 sbgrid sbgrid 1575648 Jun 27 16:55 side_chains -rwxr-xr-x 1 sbgrid sbgrid 1566208 Jun 27 16:55 side_chains_update -rwxr-xr-x 1 sbgrid sbgrid 5327984 Jun 27 16:55 solve -rwxr-xr-x 1 sbgrid sbgrid 11331152 Jun 27 16:55 solve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 6529136 Jun 27 16:55 solve_giant -rwxr-xr-x 1 sbgrid sbgrid 7729424 Jun 27 16:55 solve_huge -rwxr-xr-x 1 sbgrid sbgrid 11393392 Jun 27 16:55 solve_mx $ file phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, statically linked, for GNU/Linux 2.4.0, stripped We do have a standalone Solve install with its corresponding SOLVEDIR, etc, environment variables. Could that be confusing Phenix? I have the complete logfile, but it's rather long. If it would help, it can be made available. Any ideas on what I should do to troubleshoot this? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

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TEST - please ignore
by Luca Jovine 31 Jul '07

31 Jul '07

Sorry, just re-testing whether my e-mails to phenixbb are still vanishing into nowhere...

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A question about AutoBuild
by Marcelo Carlos Sousa 31 Jul '07

31 Jul '07

We have solved (in part) a structure by Molecular Replacement. The protein is a homodimer with 360 amino acids per chain (one dimmer per asu). The model was pretty good for the last 220 amino acids or so but appears to be wrong for the first 140 so I deleted them and refined using phenix to an R free of ~ 0.38. As I was about to start model building in O I thought I would give the phenix autobuild a try. The resolution is 2.5 Å and the map shows buildable features for the missing domain. I ran the autobuild wizard with RESOLVE building “in- place” to extend the current model. However the program seemed unable to add fragments of secondary structure (even as alanines) to the model. The question is: is the building “in-place” restricted to “growing” the current model from the ends? Marcelo

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part II. A question about autobuild
by Marcelo Carlos Sousa 31 Jul '07

31 Jul '07

I also noticed that water molecules are assigned to the buildable parts of the map.

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R-factor problem !!!
by john kryst 30 Jul '07

30 Jul '07

Hi all !! I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating. Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ?? As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us. Thanks in advance for your inputs regards John

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problems with clashes
by Lari Lehtio 30 Jul '07

30 Jul '07

Hi, I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac. In addition to the more tedious deposition (I guess), I have a problem with clashes. When I analyse the structures with molprobity, I get much better clashscores with refmac refined files. Is there a way to increase the restraint for these contacts or should I just keep decreasing the wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for bonds and angles are already lower than what I'm used to. B-factors on the other hand seem to be less restrained in phenix. ~Lari~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________

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Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 27 Jul '07

27 Jul '07

Hi Jianghai, > I tried "discard_psi_phi=False" in phenix.refine. There is only > slightly improvement in the R, Rfree, and ramachandran plot (about > 0.2% less disallowed residues, wxc_scale=0.2). A structure > optimization (wxc_scale=0) with the phi-psi restraints has a bigger > impact (about 2% less disallowed residues) with about 2% higher > Rfree. Thanks for your feedback! > What do you think is a good value for wxc_scale in a low-resolution > refinement? This is a tough one to answer. wxc_scale reflects how much you trust your data to guide you to the best model. That depends on many influences. I think the best - although expensive - approach is to simply try a range of values. Note that the esd on the psi-phi restraints are just someone's (?) best guesses. It may be worth playing with these values as well. For that, copy the data_link_TRANS, data_link_PTRANS, data_link_CIS, and data_link_PCIS blocks from mon_lib_list.cif to a new files, change the values, then specify the file on the phenix.refine command line. (You may want to double-check in the .geo file that your new values are actually used.) > What is the difference between wxc_scale=0 and > phenix.geometry_minimization? Should basically be the same, but in phenix.refine you can override parameters like discard_psi_phi. phenix.geometry_minimization doesn't allow you to do this (it is one of those many little things I never got to). Ralf

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Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 26 Jul '07

26 Jul '07

Hi Jianghai, > I am refining a low resolution huge protein structure. There are > about 20% residues in the disallowed region of ramachandran plot. Is > there a way in phenix.refine to refine the phi, psi angles to get a > better ramachandran plot? or a phi, psi restraints in refinement? If you add discard_psi_phi=False to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions. We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes! Ralf

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