[phenixbb] Issue with running phenix.segment_and_split_map command

[Philip D. Jeffrey]

Try putting a resolution=3 on the command line (change the 3 to something appropriate for you).  That omission often spawns the error you see.

(I’m not convinced that a sensible default couldn’t be deduced by the programs in many instances.)


---
Phil Jeffrey
Princeton

On Jun 10, 2023, at 12:03 PM, Das, Abhinaba <abhinaba.das at emory.edu> wrote:


Good afternoon all,

I’ve been running Phenix using the GUI however I want to segment a map using phenix.segment_and_split_map which turns out to be a command line program.

I’m trying to run it using the following command:


abhinabadas at AbhinabasM1Mac ~ % phenix.segment_and_split_map \

/Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \

/Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \

box_in_auto_sharpen = False





However, it ends every time giving the error:



Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta

Sorry: Need resolution for segment_and_split_map with sharpening





Initially, I used the same command without using auto_sharpen = False

box_in_auto_sharpen = False, as the map was already auto sharpened in Phenix. It gave me the same error regardless.



Apologies for this possibly inane question; there might be a very easy fix to it but I can’t seem to figure it out. I would greatly appreciate any insights or suggestions to resolve this issue. Please let me know if you need any further information. Thank you for your attention and assistance.



Thanks, abhi

_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20230610/225d1e51/attachment-0001.htm>