Corrected a bug in createPDB()

If the query sequence contains a gap, createPDB() was blowing up.
This bug was corrected!

gemme.py

@@ -430,7 +430,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
               "       'half-cv+pc' or max-trace-half-cv+pc!")
         sys.exit(-1)
 
-    structure = parsePDB(pdbfile)
+    structure = parsePDB(prot+".pdb")
     calphas = structure.select('name CA')
 
     chains = list(set(calphas.getChids()))

gemmeAnal.py

@@ -62,8 +62,10 @@ def createPDB(prot,seq):
 	fOUT = open(prot+'.pdb','w')
 	i = 1
 	for let in seq:
-		fOUT.write('ATOM%7d  CA  %s A%4d      43.524  70.381  46.465  1.00   0.0\n'%(i,d[let],i))
-		i += 1
+		if(let != '-'):
+			fOUT.write('ATOM%7d  CA  %s A%4d      43.524  70.381  46.465  1.00   0.0\n'%(i,d[let],i))
+			i += 1
+		
 	fOUT.close()
 
 def editConfJET(N):