On Jul 29, 2010, at 1:50 PM, Nathaniel Echols wrote:

On Thu, Jul 29, 2010 at 1:26 PM, Joseph Noel wrote:

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I noticed that coot behaves unusually on the MacOS version of phenix. It will open when you hit the button in the GUI but it will not open any of the files you specify. Just the main coot window which you then have to load everything as you would normally if running coot stand alone.

This usually means that the Python embedded in Coot isn't linked correctly (on Linux, it usually means Python wasn't even included). One way to tell is to look on the toolbar in Coot - if it doesn't have a button that says "Connected to PHENIX" (or something like that), my extension module failed. Which version are you using? I believe the most recent binary on Bill Scott's page may have this problem, but I'll double-check. I use Fink ( http://www.finkproject.org/) to install and update Coot, and this has always worked quite well as long as Fink doesn't crash on me.

Also, I noticed that when you run coot from the gui link on MacOS that after

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manipulating the structure for rebuilding, etc it will freeze requiring a force quit of x-windows to recover. However, if I open coot directly from my xterm on MacOS it works fine and no freezes. Just a note. Love the program!

This I haven't heard before. We have to tamper with the environment variables to get Coot to launch from inside Phenix, at least on Linux, and this may have side effects. Where does the console output from Coot end?

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

The root of this problem is that I fundamentally don't understand how this works. But just as a bit of background, I use fink to build the "stand-alone" coot. The only difference is that I build it in a different directory. So I would hope that if the fink version works, so should this, but apart from seeing the button appear, I really don't know how to test it. /sw/bin/coot (or the equivalent) is actually a wrapper script. The contents look like this: #!/bin/sh -f export COOT_REFMAC_LIB_DIR=/sw/share/coot/lib export COOT_PYTHON_DIR=/sw/share/coot/python export PYTHONPATH=/sw/lib/python2.6/site-packages:/sw/lib/python2.6/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH /sw/bin/coot-real "$@" I suspect PYTHONPATH needs more stuff in it. What is there is what is required for coot to find its X-windows-based python GUI dependencies. Could you try replacing the penultimate line with this and see if it works? export PYTHONPATH=$(dirname $PHENIX_BIN)/base/Python.framework/Versions/2.6/lib/python2.6:/sw/lib/python2.6/site-packages:/sw/lib/python2.6/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH If there is a better way, please let me know and I will try to fix it. Also, what is a good way to test this (keeping in mind that I am basically too stupid to operate the gui)? Thanks. Bill

vandana wrote:

hello

i have diffraction of a crystal showing Rmerge 50 % resolution 21- 3.5 A. this is due to crystal decay with time while data collection . multiplicilty is 11 .0 and data is 99.6 % complete . i want to know that is this a good data to solve structure with MR . i got solution with this data but the R factor is 46.5 and R free is 51.4 .

i want to know that if R merge is too high we should proceed to solve structure or not . Hi,

From "X-ray structure determination, a practical guide" (Stout, G.H. & Jensen, L.H. citing Wilson A.J.C. [1950], Acta Cryst. 3, 397), the expected R-factors for the atoms of the structure randomly distributed in the unit cell (or asymmetric unit) are 0.83 for centric reflections and 0.59 for acentric reflections. The values you indicate are well below the figures mentioned above, so they indicate that what you have is not random. But this is not sufficient to tell you if what you have is a proper MR solution or not: What about the packing in the unit cell? Do you have crystal-forming contacts in the 3 directions of space that explain the formation of the crystal? If there are voids, there might be molecule(s) missing. What is the value of the Z-score provided by Phaser (if you have used Phaser)? In the resulting electron density map, do you see electron density that correspond to the "mutations" you have to carry out in order to go from model to target structure? If you see such electron density, then it is very likely that you indeed have a molecular replacement solution. The value of the Rmerge (you probably mean Rsym) you give (0.5) will probably not satisfy referees for a publication. What can always be done is to use several crystals for data collection, starting data collection at different (unique) positions, and merge the resulting data (restricting the data processing to the frames where the value of Rsym is acceptable). You should then end up with a merged data set that has a lower Rmerge value. We used to do this all the time in the days prior to cryo-cooling of crystals, when crystals were mounted in capillaries. Rmerge values of 10 to 15 % were typical then. That is if the value of the Rsym is indeed due to decay. High Rsym values are also obtained in cases of crystal twinning - without proper treatment- , improper space group assignment (although in that case, much much higher values are usually observed). Fred.

Hi, Usually the data integration software lets you have several possibilities concerning the space group (at the level of the determination of the Bravais lattice, and later for the analysis of the specific extinctions). It worthwhile checking out all possibilities. I recently had a case where the auto-indexing provided the following: mC 0.1 oC 2.5 hP 4.1 P1 removed from the list. I did check everything out, and it turned out that the space group was P6(1). High Rsym values can be due to improper space group assignment. Sometimes space group specific extinctions are not that clear (or the data simply have not been recorded or cannot be processed, for example when the axis is parallel to the rotation axis). Fred.

hello fred ya i got the solution with phaser with proper packing . Space group P 6122 TFZ- 18.0 RFZ -7.8 PAK -1 LLG -282.453

density is clear and most of bulky residues are in side the density too . but while running the refinement R factor is not going down. i am trying to do fitting of the structure .

vandana kukshal