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Re: heteroatoms_zinc

I have been doing similar things with Ca ions. I don't see anything you're doing that is definitely wrong, but I do do notice that in my .ali file I have not separated the Ca by a '/' .  Also make sure the knowns are where the system can access them (that would give you an error message that would probably stop execution, so probably that's not the problem). Does 1BP3 have the Zn and all its ligands properly oriented?
John Penniston

"> wrote:
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'



  

-- 

John T. Penniston, Ph.D.
Dept. of Biochemistry and Molecular Biology
Guggenheim 16, Mayo Clinic
200 First St. SW
Rochester, MN 55905 USA