Hello, I have a following issue with running Phenix.cutout density either on command line or in GUI. I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command: phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8 Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map. In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again. Please, let me know what I am doing wrong. Thank you very much! Mikalai
Tom Terwilliger can probably add to this, because he's the author of phenix.cut_out_density. On the point of the map coefficient labels, it seems sensible that the labels for the cutout density should be different from the input ones, because it is really a different map. So I'm not surprised that there's a default to call them FWT,PHWT. I'm not sure why the map you get is not your difference map. However, there are two things that could be going on here. First, by default I think that phenix.cut_out_density recenters the cutout map on the center of the mask, so the density may simply have moved. Second, the sigma level that you have to contour the map at will be very different, so you will have to adjust the contour level to see the same features. I hope that helps to explain what you're seeing! Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 20 Sep 2012, at 11:04, Mikalai Lapkouski wrote:
Hello,
I have a following issue with running Phenix.cutout density either on command line or in GUI.
I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command:
phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8
Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map.
In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again.
Please, let me know what I am doing wrong.
Thank you very much!
Mikalai
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Hi Mikalai, I'm sorry for the trouble! If cut_out_density is taking the wrong map coefficients from your file, could you possibly send me the mtz file (off-list, [email protected]) and any other inputs you are using, and I'll check it out here? Or if you can just send me the full log file, that might help too. Thanks very much! -Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Randy Read [[email protected]] Sent: Thursday, September 20, 2012 5:56 AM To: PHENIX user mailing list Subject: Re: [phenixbb] Phenix cut out density labels choice Tom Terwilliger can probably add to this, because he's the author of phenix.cut_out_density. On the point of the map coefficient labels, it seems sensible that the labels for the cutout density should be different from the input ones, because it is really a different map. So I'm not surprised that there's a default to call them FWT,PHWT. I'm not sure why the map you get is not your difference map. However, there are two things that could be going on here. First, by default I think that phenix.cut_out_density recenters the cutout map on the center of the mask, so the density may simply have moved. Second, the sigma level that you have to contour the map at will be very different, so you will have to adjust the contour level to see the same features. I hope that helps to explain what you're seeing! Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 20 Sep 2012, at 11:04, Mikalai Lapkouski wrote:
Hello,
I have a following issue with running Phenix.cutout density either on command line or in GUI.
I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command:
phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8
Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map.
In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again.
Please, let me know what I am doing wrong.
Thank you very much!
Mikalai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Mikalai Lapkouski -
Randy Read -
Terwilliger, Thomas C