src/hg/lib/lsSnpPdbChimera.py 1.4

Index: src/hg/lib/lsSnpPdbChimera.py
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/lsSnpPdbChimera.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/lib/lsSnpPdbChimera.py	5 Feb 2009 08:04:11 -0000	1.3
+++ src/hg/lib/lsSnpPdbChimera.py	13 May 2009 19:05:17 -0000	1.4
@@ -1,42 +1,46 @@
 # if you are seeing this file as text in a web browser, you need to configure
 # chimerax as a helper application.
 
 # Python code for chimerax files to display proteins with SNPs annotated.
 # Due scoping bug in exec coding from chimerax files (1.3 alpha release and
 # earlier), can only have one function and must import into function's local
 # namespace.
 
-def displayPdb(pdbId, snps):
-    # snps is list of (snpId, chain, snpPos, [isPrimary])
+def displayPdb(pdbSpec, snps):
+    """pdbSpec can be a pdbId or a URL of a PDB format file.
+    snps is list of (snpId, chain, snpPos, [isPrimary])"""
     from chimera import runCommand
     from chimera.selection import OSLSelection
     runCommand("close all")
-    runCommand("open pdb:%s" % pdbId)
+    if pdbSpec.find("://") >= 0:
+        runCommand("open %s" % pdbSpec)
+    else:
+        runCommand("open pdb:%s" % pdbSpec)
 
     # hide all models/sub-models, NMR will only show first model
     runCommand("select #*:*.*")
     runCommand("~display sel")
     runCommand("~select")
 
     # get model spec to use, testing for sub-models, as is the case with NMR
     sel = OSLSelection("#0.1")
     if len(sel.atoms()) > 0:
         modelSpec = "#0.1"
     else:
         modelSpec = "#0"
     caSpec = "%s:.*@CA" % modelSpec
 
     # display ribbons
     runCommand("ribbon %s" % caSpec)
     runCommand("ribbackbone %s" % caSpec)
     runCommand("focus %s" % caSpec)
 
     for snp in snps:
         (snpId, chain, snpPos) = snp[0:3]
         if ((len(snp) > 3) and snp[3]):
             color = "red" 
         else:
             color = "gold"
         spec = "%s:%s.%s@CA" % (modelSpec, snpPos, chain)
         runCommand("color %s %s" % (color, spec))
         runCommand("setattr r label \"%s\" %s" % (snpId, spec))