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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 30 Jul '07

30 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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ramachanran plot refinement or restraint?
by Jianghai Zhu 26 Jul '07

26 Jul '07

Hi, 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? Thanks. 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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problems in installation of phenix
by tara kashav 25 Jul '07

25 Jul '07

Dear all, I am trying to install phenix but getting following error. My system specifications are: 2.6.5-1.358 i686. Can anyone suggest me how to troubleshoot and install the program. Traceback (most recent call last): File "/usr/local/phenix-1.3b/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libXfixes.so.3: cannot open shared object file: No such file or directory Thanks, Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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Re: [phenixbb] How to keep a custom bond planar ?
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Mathieu, Also sorry for the late reply. > How can I define a plan or some dihedral ?? Sorry, this is not implemented (not hard, but never got to it). > Or as in the ligand .cif I defined a plan > LIG plan-2 C1 0.020 > LIG plan-2 C2 0.020 > LIG plan-2 C3 0.020 > > I could add the atoms NZ and CE of the lysine to the plan-2. You can define the bond, angles, dihedrals, chiralities and planarities with a cif link. Currently we don't generate such links automatically (it is in the works). To get a start, copy one of the links from the mon_lib_list.cif file; the command phenix.where_mon_lib_list_cif will give you the absolute path. Give the cif link a unique name and modify it for your situation. Then use "apply_cif_link" as described in the phenix.refine documentation, e.g. at the CCI Apps download page (http://www.phenix-online.org/download/cci_apps/). Let me know if you need more specific help. Ralf

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Re: [phenixbb] handling of alternate conformations
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Ulrich, Sorry for the late reply. I was out of town for a week. > My first question is whether NCS constraints are also applied to alternate > conformations. Should be, but is not heavily tested. All NCS restraints are listed in the .geo file created by phenix.refine (assuming write_geo_file=True, which is the default). Look for the long lists following "NCS restraint group". Do your alternative conformation atoms appear in these lists? > My second question concerns the atom count of the conformers, where the > parts with non-alternating conformations seem to be included as well. Pavel's explanation from last week is correct. Internally a "conformer" is always a complete chain. The bond, angle, dihedral, chirality, and planarity restraints are determined independently for each conformer. This generates duplicate restraints which are checked for consistency and then reduced again. Ralf

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