Greetings, I am trying to run focus_alignment command ( https://pymolwiki.org/index.php/Focus_alignment) from within a Python script with my own custom selection (I include CA+CB atoms instead of only CA as in the default). Sometimes the selection is very large and PyMOL cannot hand it:
Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Invalid selection name "730". > poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730<-- > Selector-Error: Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "868". > poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868<-- > ExecutiveRMS-Error: No atoms selected. > Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "730". > ( ( poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730 ) in ( poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868 ) )<-- Is there a way to ask PyMOL to accept longer selection strings? Alternatively, is it possible to catch this exception from within the script using "try: ... except <some exception>:" statement? Thanks in advance. Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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