map woes from refine
Y'all, Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file. I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason? Any help appreciated. Cheers, MM
Hi Mischa, an industry user reported the same problem a few days ago but he could not send the data. So I really hope you can send me the files (data and model) so I can reproduce and fix this problem - this would be a huge help. There must be an obscure bug somewhere introduced in recent (after release) versions, but I can't figure out what it is. Thanks, Pavel On 3/6/13 12:13 PM, Machius, Mischa Christian wrote:
Y'all,
Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file.
I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason?
Any help appreciated.
Cheers, MM _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
We are having exactly the same issue. Loading the "no_fill" map coefficents
manually gives a much more sensible map, but the map loaded from the GUI or
auto open mtz from coot looks exactly as Mischa is describing it. I can
confirm that this happens with 1312 and 1314 development builds.
--Dave
On Wed, Mar 6, 2013 at 3:24 PM, Pavel Afonine
Hi Mischa,
an industry user reported the same problem a few days ago but he could not send the data. So I really hope you can send me the files (data and model) so I can reproduce and fix this problem - this would be a huge help. There must be an obscure bug somewhere introduced in recent (after release) versions, but I can't figure out what it is.
Thanks, Pavel
On 3/6/13 12:13 PM, Machius, Mischa Christian wrote:
Y'all,
Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file.
I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason?
Any help appreciated.
Cheers, MM ______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb
______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb
Hi Mischa, thanks for sending the files. I can reproduce the problem and I'm working on the fix. I will post an update once the problem is fixed. Pavel On 3/6/13 12:13 PM, Machius, Mischa Christian wrote:
Y'all,
Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file.
I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason?
Any help appreciated.
Cheers, MM _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hello, anyone who experienced this problem please try the latest build: http://www.phenix-online.org/download/nightly_builds.cgi I was able to reproduce the problem using Mischa's data (many thanks Mischa !) and fix it. Please let me know should you see any problem. Thanks, Pavel On 3/6/13 12:13 PM, Machius, Mischa Christian wrote:
Y'all,
Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file.
I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason?
Any help appreciated.
Cheers, MM _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Dave Lodowski -
Machius, Mischa Christian -
Pavel Afonine