Hi, I have one question and one problem. TEXTAL expects map in X-PLOR format but what kind of map? One can make a number of different maps in CCP4 (simple, mFo-nFc, etc.). Which type make TEXTAL happy? I've tried to run 'Build Complete Model from map' strategy and what ever I do it seems to get stuck at: Stitching and Filtering C-alpha chains... - simply nothing happens anymore. What could be a problem? Just to mention it does build a model when I use '... from mtz' strategy. MfG, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery
On Tue, 9 May 2006, Andrzej LYSKOWSKI wrote:
Hi,
I have one question and one problem.
TEXTAL expects map in X-PLOR format but what kind of map? One can make a number of different maps in CCP4 (simple, mFo-nFc, etc.). Which type make TEXTAL happy?
Textal can deal with simple maps, back-transformed (Fc), and 2Fo-Fc maps. One can also make such maps with phenix.refine, textal.makemap, or various map-making tasks in the phenix GUI
I've tried to run 'Build Complete Model from map' strategy and what ever I do it seems to get stuck at: Stitching and Filtering C-alpha chains... - simply nothing happens anymore. What could be a problem? Just to mention it does build a model when I use '... from mtz' strategy.
Is it possible to get the log up to this point? Also, are there any error messages in the terminal window where you started phenix? Could you also try running this same map through textal.from_map (textal.from_map my.xplor)? Thanks Erik
TEXTAL expects map in X-PLOR format but what kind of map? One can make a number of different maps in CCP4 (simple, mFo-nFc, etc.). Which type make TEXTAL happy?
Textal can deal with simple maps, back-transformed (Fc), and 2Fo-Fc maps. One can also make such maps with phenix.refine, textal.makemap, or various map-making tasks in the phenix GUI
Just to mention: if you run the command % phenix.refine data.mtz model.pdb by default it will perform some model refinement (3 macro-cycles) and will write out two maps mFo-DFc and 2mFo-DFc in XPLOR format. If you don't want any refinement to be performed, just type: % phenix.refine data.mtz model.pdb main.number_of_macro_cycles=1 main.refine_site=false main.refine_adp_individual=false this will do the anisotropic scaling, bulk solvent modeling, calculation of m and D, and finally writing out two maps mFo-DFc and 2mFo-DFc. For more info and options look phenix.refine documentation at http://www.phenix-online.org/download/cci_apps/ Thanks for your questions, Pavel.
participants (3)
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Andrzej LYSKOWSKI -
Erik Mckee -
Pavel Afonine