Re: [phenixbb] Let's talk about maps...
Hi Pavel, It would be really nice if the Electron density maps section in the online docs for phenix.refine http://www.phenix-online.org/documentation/refinement.htm#anch70 was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb. Mark --
Hi Mark, thanks! Yes, I think so. I will add this to the documentation. Pavel. On 8/6/09 3:08 PM, Dr. Mark Mayer wrote:
Hi Pavel,
It would be really nice if the Electron density maps section in the online docs for phenix.refine
http://www.phenix-online.org/documentation/refinement.htm#anch70
was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb.
Mark
I changed my refine def file to read: map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } and I get the error: n_use = 1159 n_use_u_iso = 1159 n_use_u_aniso = 1141 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 1141 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 1141 total number of scatterers = 1159 Sorry: Duplicate mtz_label_amplitudes:2FOFCWT at the end of refinement. Did I do something wrong? thanks FR On Aug 6, 2009, at 4:13 PM, Pavel Afonine wrote:
Hi Mark,
thanks! Yes, I think so. I will add this to the documentation.
Pavel.
On 8/6/09 3:08 PM, Dr. Mark Mayer wrote:
Hi Pavel,
It would be really nice if the Electron density maps section in the online docs for phenix.refine
http://www.phenix-online.org/documentation/refinement.htm#anch70
was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb.
Mark
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, yes, you need to re-name the labels too, for example: mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" pheni.refine writes the map with 2FOFCWT coefficients by default, and below you specified another additional map with the same coefficients, so there is a conflict. I know it is annoying and several people faced this problem before, so I will make this automatic in the future. Pavel. On 8/7/09 7:27 AM, Francis E Reyes wrote:
I changed my refine def file to read: map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True }
and I get the error:
n_use = 1159 n_use_u_iso = 1159 n_use_u_aniso = 1141 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 1141 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 1141 total number of scatterers = 1159
Sorry: Duplicate mtz_label_amplitudes:2FOFCWT
at the end of refinement. Did I do something wrong?
thanks
FR
On Aug 6, 2009, at 4:13 PM, Pavel Afonine wrote:
Hi Mark,
thanks! Yes, I think so. I will add this to the documentation.
Pavel.
On 8/6/09 3:08 PM, Dr. Mark Mayer wrote:
Hi Pavel,
It would be really nice if the Electron density maps section in the online docs for phenix.refine
http://www.phenix-online.org/documentation/refinement.htm#anch70
was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb.
Mark
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Ran into this last week too... You need to change the labels to 2FOFCWT_K and PH2FOFCWT_K I hope Pavel is realizing that the current way is not optimal and is changing the code to make it less error prone. Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Francis E Reyes Sent: Friday, August 07, 2009 10:28 AM To: PHENIX user mailing list Subject: [phenixbb] Enabling kicked maps...
I changed my refine def file to read: map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True }
and I get the error:
n_use = 1159 n_use_u_iso = 1159 n_use_u_aniso = 1141 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 1141 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 1141 total number of scatterers = 1159
Sorry: Duplicate mtz_label_amplitudes:2FOFCWT
at the end of refinement. Did I do something wrong?
thanks
FR
On Aug 6, 2009, at 4:13 PM, Pavel Afonine wrote:
Hi Mark,
thanks! Yes, I think so. I will add this to the documentation.
Pavel.
On 8/6/09 3:08 PM, Dr. Mark Mayer wrote:
Hi Pavel,
It would be really nice if the Electron density maps section in the online docs for phenix.refine
http://www.phenix-online.org/documentation/refinement.htm#anch70
was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb.
Mark
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Dr. Mark Mayer -
Francis E Reyes -
Pavel Afonine -
Schubert, Carsten [PRDUS]