We will have a .atm file with the x,y,z co-codinates of the desired protein. If the sequence is subjected to some modifications (alignment correction), we will get a new coordinate file (.atm). Now in the "subject or the query part of . ali" file, how do we have to define the number of amino acids in sequence?
.atm file : 2 to 149 amino acids
modified .atm file : 2 to 149 amino acids ( but 4 amino acids are removed in the middle)
now in .ali file how we have to mention at the place of template/ subject region ?
(1) we have extracted the x,y,z co'ordinates that are required, from a pdb file and saved in ".atm file " with the length 2 to 149
(2) Then we have "removed 4 amino acids in .atm file-16th,17th,18th & 19th amino acids " for the ALIGNMENT CORRECTION.
(3) Now What are the numbers that we have to mention at the place of template / subject in ".ali file" ( we are getting error if we mention 2 to 149 in the template place of ".ali file")
what is the error u r getting??? cn u send me ur *.ali and *.atm file.
My email id is: [email protected]
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