Hi all,
i'm trying to get modeller to include a zinc atom in my model. I have mastered the art ofgetting teh zinc read into the program, however the model it produces has the zinc miles away and the
coordinating residues stubbornly unligated.
How does one go about instructing modeller to coordinate the zinc atom. I have a histine and a asp coordinating it.
i have attached my alignment and inputfiles
regards
Alys
[pei015@freedom model_zinc]$ more xmera_1.ali
P1;1BP3
structureX:1BP3: 214 :A: 413 :A:undefined:undefined:-1.00:-1.00
---------------SPNKE-TF/--------------------
-------HREG--ETLM/---------------------------HFGKQYTS--MWRT/-------------------------
-----------YVDVTY/-------------------------------LIDLKTGWFT/---------------
------------FAG-Q/--------------------------KP--DHGY/----------------------/z*
P1;1N26
structureX:1N26: 92 :A: 299 :A:undefined:undefined:-1.00:-1.00
DVP--PEEPQL-SCF--------RKSPLSNVVCEWGPRSTPSLT
TKAVLLV----------RKFQNSPAEDFQEPCQY--SQESQKFSC--------------QL---AVPEGDSSFYIVSMCVASSVG
SKFS----KTQTFQGCGILQPDPPANITVTAVAR--NPRWLSVTWQDPH----------SWNSS-F-YRLRFELR
YRAERSKTFTTW------MVKDLQHHCVIHDAWSGLRHVVQLRA--------QEEFGQGEWSEWSPEAMGTPWTES/-*
P1;1xmera
sequence:1xmera: : : : :undefined:undefined:-1.00:-1.00
DVP--PEEPQL-SCFSPNKE-TF--------VCEWGPRSTPSLT
TKAVLLVHREG--ETLM----------FQEPCQY--SQESQKFSCHFGKQYTS--MWRT--------------YIVSMCVASSVG
SKFS----DELYVDVTYILQPDPPANITVTAVAR--NPRWLSVTWQDPHLIDLKTGWFT----------LRFELR
YRAERSKTFTTWFAG-Q------QHHCVIHDAWSGLRHVVQLRAKP--DHGY--------WSEWSPEAMGTPWTES/z*
the top file is
[pei015@freedom model_zinc]$ more build_model.top
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'xmera_1.ali'
SET KNOWNS = '1BP3' '1N26'
SET SEQUENCE = '1xmera'
SET HETATM_IO = on
CALL ROUTINE = 'model'