Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy Am I missing something obvious? Alternately, If anyone can share a script I would prefer it! many thanks Veronica
I remember there was a thread about this. The conclusion is to use FEM instead of kickmap, if I remember correctly. Wei On Thu, Nov 24, 2016 at 12:29 PM, Veronica Fiorentino < [email protected]> wrote:
Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy
Am I missing something obvious? Alternately, If anyone can share a script I would prefer it!
many thanks Veronica _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Veronica, Dusan's "kick maps" idea has evolved into something better (we hope) that we call FEM (Feature Enhanced Maps)[*]. Reading is available here: http://journals.iucr.org/d/issues/2015/03/00/lv5075/lv5075.pdf You can use the too from Phenix GUI or command line (phenix.fem). Let us know should you have any questions or problems! Pavel [*] This is still experimental and ongoing. Significant improvements to this tool are envisaged in future. On 11/24/16 09:29, Veronica Fiorentino wrote:
Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy
Am I missing something obvious? Alternately, If anyone can share a script I would prefer it!
many thanks Veronica _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Dusan's "kick maps" idea has evolved into something better (we hope) that we call FEM (Feature Enhanced Maps)[*].
Reading is available here:
Let us know should you have any questions or problems!
Thanks a lot. I did use FEM and they look good. My real aim: In my structure there is a loop that looks complteley different to homologus published PDB structures. Can I use a FEM (2mFo -Fc) and show the density at 2Sigma to prove that my loop is distinct and real (away from model bias). I also made a AutoBuild-Iterative-Buiild-Composite-Omit-Map that produced a resolve-composite-map.mtz (shows same loop density). What sigma level should I display these maps in a paper? I did look at pavel_maps.PDF but confused as there are so many numbers. Thanks a lot. -V
Pavel
[*] This is still experimental and ongoing. Significant improvements to this tool are envisaged in future.
On 11/24/16 09:29, Veronica Fiorentino wrote:
Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy
Am I missing something obvious? Alternately, If anyone can share a script I would prefer it!
many thanks Veronica _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Hi Veronica, sounds like you collected plenty of evidence for that loop! By construction of FEM you can use any contouring level. Pavel On 11/25/16 03:24, Veronica Fiorentino wrote:
Dusan's "kick maps" idea has evolved into something better (we hope) that we call FEM (Feature Enhanced Maps)[*].
Reading is available here:
Let us know should you have any questions or problems! Thanks a lot. I did use FEM and they look good. My real aim: In my structure there is a loop that looks complteley different to homologus published PDB structures. Can I use a FEM (2mFo -Fc) and show the density at 2Sigma to prove that my loop is distinct and real (away from model bias). I also made a AutoBuild-Iterative-Buiild-Composite-Omit-Map that produced a resolve-composite-map.mtz (shows same loop density). What sigma level should I display these maps in a paper?
I did look at pavel_maps.PDF but confused as there are so many numbers. Thanks a lot.
-V
Pavel
[*] This is still experimental and ongoing. Significant improvements to this tool are envisaged in future.
On 11/24/16 09:29, Veronica Fiorentino wrote:
Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy
Am I missing something obvious? Alternately, If anyone can share a script I would prefer it!
many thanks Veronica _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
participants (3)
-
Pavel Afonine -
Veronica Fiorentino -
Wei Wang