Changes between Version 19 and Version 20 of Release1.4

Timestamp:

Nov 24, 2008, 4:59:02 PM (17 years ago)

Author:

meng

Comment:

--

Release1.4

@@ -79 +79 @@
 
  * connect to our own Web service to BLAST on PDB, provide dialog for choosing which hit structures to open, whether to show pairwise sequence alignment from BLAST (in MAV), whether to superimpose hit and query structures (with Matchmaker). Input is sequence of molecule model already open in Chimera. ECM
-    * (search other databases such as NR? PSI-BLAST on NR?)
- * connect to our own Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see [http://www.cgl.ucsf.edu/home/meng/sources.html#d list and links]), show result in MAV. I guess input to server would be sequence alignment sent from MAV, probably would have to reformat into unaligned multi-FASTA. ECM
+    * (search other databases such as NR? PSI-BLAST on NR?) 
+
+ * connect to our own Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see [http://www.cgl.ucsf.edu/home/meng/sources.html#d list and links]), show result in MAV. Input would be sequence alignment already open in Chimera, probably would have to reformat into unaligned multi-FASTA for server. ECM
+
  * allow editing sequence name. ECM
- * allow specifying sequence to add by accession (Uniprot perhaps?).  Its feature annotations would automatically come along as regions.  ECM
-    * would we want Fetch by ID for sequences? (would we want a sequence with no structure not aligned with any other sequences?)
- * for existing sequences, allow specifying Uniprot accession for annotation retrieval, parse XML, load feature annotations as sequence regions.  (actually I don't know if that would work - what if the existing sequence and that uniprot sequence were even slightly different?) ECM
+
+ * allow specifying "sequence to add" by accession (GI number? Uniprot accession?). Its feature annotations would automatically come along as regions.  ECM
+    * would we want Fetch by ID for sequences? (would we want a sequence with no structure and not aligned with any other sequences?)
+
+ * for existing sequences, allow specifying accession for annotation retrieval, load feature annotations as sequence regions (actually I don't know if that would work - what if the existing sequence and that database sequence were even slightly different?) ECM
+
  * easier reporting of amino acid phi,psi,omega,chiN (perhaps this is Chimera core but one could imagine some connection to Multalign Viewer since it only applies to peptide/protein sequences). ECM