Converting .mtz to xplor or having phenix output to xplor file
Hi, This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format. Thanks! -Sam
Hi Sam You can use ccp4 maps in pymol if they have the extension .ccp4 (map.ccp4). You can generate these maps from mtz files using ccp4i (map and mask utilities, create maps). Output the map in ccp4 format to cover your pdb file. You might have to rename the output file. Sue On Oct 27, 2009, at 2:28 PM, Sam Stampfer wrote:
Hi,
This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format.
Thanks! -Sam _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 [email protected] http://www.biochem.arizona.edu/xray
On Oct 27, 2009, at 2:28 PM, Sam Stampfer wrote:
This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format.
Several solutions: 1) phenix.create_maps 2) output.write_maps=True in phenix.refine will generate XPLOR maps. 3) In the GUI, it should create the XPLOR maps on the fly if you click one of the "Open in PyMOL" buttons. Since most of the necessary code is already floating around, I don't mind creating a utility for simply converting map coefficients, if people would find this useful, but unfortunately we don't have the ability to write CCP4-format maps yet. One thing to make sure of is that PyMOL is recognizing the input format correctly - sometimes you need to explicitly state this: PyMOL> load 2fofc.xplor, format=xplor ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Thanks- got it working! I used #2 (redid the refinement).
-Sam
On Tue, Oct 27, 2009 at 5:54 PM, Nathaniel Echols
On Oct 27, 2009, at 2:28 PM, Sam Stampfer wrote:
This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format.
Several solutions:
1) phenix.create_maps
2) output.write_maps=True in phenix.refine will generate XPLOR maps.
3) In the GUI, it should create the XPLOR maps on the fly if you click one of the "Open in PyMOL" buttons.
Since most of the necessary code is already floating around, I don't mind creating a utility for simply converting map coefficients, if people would find this useful, but unfortunately we don't have the ability to write CCP4-format maps yet.
One thing to make sure of is that PyMOL is recognizing the input format correctly - sometimes you need to explicitly state this:
PyMOL> load 2fofc.xplor, format=xplor
------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Sam, two ways: - ask phenix.refine to output X-plor formatted map. For example, to run phenix.refine just to compute the map: phenix.refine model.pdb data.mtz main.number_of_mac=1 strategy=none write_maps=true - use "Create maps" option from main PHENIX GUI that will alow you to compute any map. Pavel. On 10/27/09 2:28 PM, Sam Stampfer wrote:
Hi,
This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format.
Thanks! -Sam ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
When I did phenix run, it made .map files that were not readable in my Pymol. I don't know this is the case for everybody. However, once I changed .map to .xplor, there was no problem.
Another follow up questions is how you can make difference map with positive and negative density maps showed up separately or together in Pymol as we see on the coot.
Thanks in advance,
YoungJin
----- Original Message -----
From: "Pavel Afonine"
On Oct 28, 2009, at 10:58 AM, Young-Jin Cho wrote:
When I did phenix run, it made .map files that were not readable in my Pymol. I don't know this is the case for everybody. However, once I changed .map to .xplor, there was no problem.
This is why you need to do this: PyMOL> load something.map, format=xplor Otherwise, it assumes that the extension .map is a different format (not sure which one, but definitely not XPLOR).
Another follow up questions is how you can make difference map with positive and negative density maps showed up separately or together in Pymol as we see on the coot.
isomesh neg_diff, map_name, -3.0 isomesh pos_diff, map_name, 3.0 Although you're probably going to want to add another parameter for the selection to draw around, otherwise I think it tries to draw the entire map, which is often too much for the graphics card to handle. Unfortunately, the way it deals with re-centering and maps isn't very robust compared to Coot. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (5)
-
Nathaniel Echols -
Pavel Afonine -
Sam Stampfer -
Sue Roberts -
Young-Jin Cho