Package: pymol / 2.4.0+dfsg-2

34_fix_examples_add_fetch_instead_of_load.patch Patch series | download
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Author: Tatiana Malygina <merlettaia@gmail.com>
Description: use fetch instead of load in pymol scripts when necessary
 In example scripts, which require .pdb files not shipped with upstream source,
 use fetch instead of load, to download required Protein Data Bank structures.
 .
 See more on pymol's `fetch` command here: 
 http://www.pymolwiki.org/index.php/Fetch
Last-Update: 2016-08-16

--- a/examples/cookbook/contact.pml
+++ b/examples/cookbook/contact.pml
@@ -1,6 +1,7 @@
 # load pdb file which has a CRYST1 record
 
-load 1DN2.pdb,1dn2
+fetch 1DN2, async=0
+# load 1DN2.pdb,1dn2
 
 # create neighbor with contact near a certain atom
 
--- a/examples/cookbook/packing.pml
+++ b/examples/cookbook/packing.pml
@@ -1,6 +1,7 @@
 # load pdb file which has a CRYST1 record
 
-load 1DN2.pdb,1dn2
+fetch 1dn2, async=0
+# load 1DN2.pdb,1dn2
 
 # create neighbors with contacts
 
--- a/examples/cookbook/packsurf.pml
+++ b/examples/cookbook/packsurf.pml
@@ -1,6 +1,7 @@
 # load pdb file which has a CRYST1 record
 
-load 1DN2.pdb,1dn2
+fetch 1dn2, async=0
+# load 1DN2.pdb,1dn2
 
 # remove waters 
 
--- a/examples/cookbook/ref_frame.pml
+++ b/examples/cookbook/ref_frame.pml
@@ -1,9 +1,9 @@
 
 # load structures
-
-load 1btu.pdb, 1btu
-load 1ce5.pdb, 1ce5
-load 1vgc.pdb, 1vgc
+fetch 1btu 1ce5 1vgc, async=0
+# load 1btu.pdb, 1btu
+# load 1ce5.pdb, 1ce5
+# load 1vgc.pdb, 1vgc
 
 # separate the ligands
 
@@ -30,4 +30,3 @@ save 1ce5_1vgc.pdb, 1vgc, ref=1ce5
 save 1ce5_1ce5_lig.pdb, 1ce5_lig, ref=1ce5
 save 1ce5_1btu_lig.pdb, 1btu_lig, ref=1ce5
 save 1ce5_1vgc_lig.pdb, 1vgc_lig, ref=1ce5
-
--- a/examples/cookbook/ribosome.pml
+++ b/examples/cookbook/ribosome.pml
@@ -1,9 +1,10 @@
-load 1FFK.pdb,1ffk
+fetch 1ffk, async=0
+# load 1FFK.pdb,1ffk
 
 # create object with only nucleic acid
 
 create nuc = (1ffk and not n;ca,cd)
-del 1ffk
+remove 1ffk
 
 # color contiguous chains
 
--- a/examples/cookbook/ss_xfer.pml
+++ b/examples/cookbook/ss_xfer.pml
@@ -1,10 +1,12 @@
 
 # ss_xfer.pml:  Copies secondary structure from a source protein
 # over to a target protein.  Residue identifiers must match perfectly.
-
-load 1t46.pdb, source
-
-load 1pkg.pdb, target
+fetch 1t46, async=0
+copy source, 1t46
+#load 1t46.pdb, source
+fetch 1pkg, async=0
+copy target, 1pkg
+#load 1pkg.pdb, target
 
 # remove all secondary structure assignments
 
@@ -31,7 +33,3 @@ alter target and polymer and name CA, ss
 # rebuild the cartoon
 
 rebuild
-
-
-
-