bugs

scop units without chain number will not shown
scop units without chain number was not in id_pdb_ch_fr_to.txt nor in pdbsum folder.
pdbsum's website's change affected chain# labeling.

plan

PLAN
1/25/05

1. The paper : supersecondary structure of sandwich
a) Write about your part : calculation and presentation 1/25/05
b) find structures with parallel strands
c) find structures with more than two sheets.
2. Project our database “SS”
Think about,
Check database TOPS 1/25/05
3. supersecondary structure of barrel 1/25/05
a. extract from database antiparallel barrel only 1/25/

1/27/05
1) extract “perfect” barrel 1/27/05 (simple, no side chain, closed).
b. Present arrangement of strand in excel format
c. Separate two sub-sheets for barrel

2/1/05
1. Poster at ISCB
2. Write a section: Methods (what was done and what you calculated the result is “database”)
3. THINK how to improve the presentation: parallel/antiparallel and the order of strands in a sheet.
1 3 5 7
2 4 6 8 the strand 1 and 2 are close to each other

4. urgent sandwich only a) list (PDB codes) of two sheets only with antiparallel strands only
b) list (PDB codes) of three and more sheets with antiparallel strands only
c) list (PDB codes) where parallel strands is occurred.

a) 1bbb
1ccc (A:233-444)
b) 1bbb (3+4) means strands 3 and 4 form separate sheet
c) 1bbb (3 4 ) strands 2 and 4 are parallel.

2/8/05

analysis with the Table – define motif and supermotifs for each reperesentative
Mark starts with fold #2, … determine strands
AK analyzes Ig fold

2/22/05
1. prepare the draft for the meeting
2. database
a) question about server
b) domain space for database, and domain name. (Adam)
c) make correct orientation, and show parallel strands.
d) Mention the correction we did for our data. Ex: missed strands, minimize the lowest strand number to 1.
e) Separate the graph to a popup window.
f) Write a description about our database
g) Difference with others.
3. file statistics continue.

parallel/antiparallel database

you can query by pdbid here
http://oca.ebi.ac.uk/oca-bin/csu?PDB_ID=1l6z

or you can read pdb file accourding to columns 39-40 in pdb's doc
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html

I think I'll use subgraph in P.26 in this document
instead of yEd, since graphviz is free.

I tried to use yEd to generate the graph Kister want.
we need to add one dummy at both end of the sandwich connect to the edge strand of both sheets, and add one group at the interlock on both sheet, and add one group contents each sheet.
Then, run the Organic-classic layout.
Then, remove two dummies, and delete group on interlocks.
you'll get a pretty good result.

BUT, yEd is commercial software, which cost $$$.

There are 7797 scops for sandwichs (folds #1~#42) in my DB.

after I analysis 30 scops, I got these conclutions:

S1 will belong to one sheet, S2 will belong to another.
S2 will connect to the last Strand.
this is the start and the end strand, they are in one edge of the sandwich, and used for connect two sheets.
the other side of the sandwich are connected by a loop.

only found one exception ([88535]1cd0A), but kind of acceptable.

PLAN
1/25/05

1. The paper : supersecondary structure of sandwich
a) Write about your part : calculation and presentation 1/25/05
b) find structures with parallel strands
c) find structures with more than two sheets.
2. Project our database “SS”
Think about,
Check database TOPS 1/25/05
3. supersecondary structure of barrel 1/25/05
a. extract from database antiparallel barrel only 1/25/

1/27/05
1) extract “perfect” barrel 1/27/05 (simple, no side chain, closed).
b. Present arrangement of strand in excel format
c. Separate two sub-sheets for barrel

2/1/05
1. Poster at ISCB
2. Write a section: Methods (what was done and what you calculated the result is “database”)
3. THINK how to improve the presentation: parallel/antiparallel and the order of strands in a sheet.
1 3 5 7
2 4 6 8 the strand 1 and 2 are close to each other

4. urgent sandwich only a) list (PDB codes) of two sheets only with antiparallel strands only
b) list (PDB codes) of three and more sheets with antiparallel strands only
c) list (PDB codes) where parallel strands is occurred.

a) 1bbb
1ccc (A:233-444)
b) 1bbb (3+4) means strands 3 and 4 form separate sheet
c) 1bbb (3 &4 ) strands 2 and 4 are parallel.

http://www.iscb.org/ismb2005/poster_call.html