Feature Requests item #1656702, was opened at 2007-02-10 07:19
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1656702&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Interface Improvements
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Angel Herraez (aherraez)
>Assigned to: Bob Hanson (hansonr)
Summary: molecule name shown for PDB
Initial Comment:
A proposal to retrieve and use some molecule name from PDB files to be shown in
Jmol title and menu.
Current state:
** With MOL files:
- Jmol app window title: shows the filename + extension, followed by a dash and
the contents of line 1 (which usually is the molecule name or description).
- Both app and applet: show the molecule name (line 1) as the topmost entry in
the popup menu.
- Applet: shows the filename as the bottommost sub-entry inside the former.
If line 1 is empty, defaults to filename.
** With PDB files, the same degree of information would be desirable. However,
currently only the filename is used:
- Jmol app window title: shows the filename + extension, followed by a dash and
(again) the filename without extension.
- Both app and applet: show the filename (without extension) as the topmost
menu entry in the popup menu.
- Applet: shows the filename + extension as the bottommost sub-entry inside the
former.
Proposal: interpret the molecule name or description in the PDB file and use it
similarly to what is done for MOLfiles' 1st line. Current use of the filename
is redundant.
I'm not an expert on PDB format, and the structure of PDB entries is varied, so
this is open to discussion and likely to need quite a parsing. There are
candidate fields: COMPND, TITLE, HEADER; if one is missing, another could take
its place.
HEADER is the easiest and seems logical, but it tends to contain a generic name
or cathegory often not specific to the molecule (e.g. "Hydrolase(O-Glycosyl)"
for lysozyme 123L.pdb); I'd prefer COMPND.
1) If "COMPND 2 MOLECULE:" field is present, use it; extract portion after
MOLECULE: up to semicolon.
2) Else, use first line with "COMPND" field.
3) Else, use HEADER (trimming the deposition date and pdbcode).
4) Else, use TITLE (maybe trimmed, tends to be too long).
5) Use filename if the others fail.
----------------------------------------------------------------------
>Comment By: Bob Hanson (hansonr)
Date: 2007-02-13 09:58
Message:
Logged In: YES
user_id=1082841
Originator: NO
OK, I looked into this some more.
PDB files:
The model name is derived from the four-digit PDB designation from columns
63-66 of the PDB header line.
This is what is showing up in the app title after the dash and in the
pop-up menu top line.
mmCIF files:
The model name is derived from the "data" line as in
data_1MBO
So this isn't a redundancy, really. The files just happen to be named this
way usually.
The two places that would make sense for this information would be the
very top line of the first
submenu item, the one with the 4-digit PDB designation.
CIF files: Maybe we should start with these, because they are more
standardized.
There is a standard block _struct
_struct.entry_id 1XY2
_struct.title
;CRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL
FLEXIBILITY AND RECEPTOR BINDING
;
_struct.pdbx_descriptor '1 BETA-MERCAPTOPROPIONATE-OXYTOCIN (DRY
FORM)'
Of these, entry_id is required; title is not. So that's fine.
In addition, we have:
loop_
_pdbx_entity_name.entity_id
_pdbx_entity_name.name
_pdbx_entity_name.name_type
1 "PLASTOCYANIN" 'SWS-NAME'
1 "Electron transport" 'SWS-KEYWORD'
I think you can see that the PDB information from HEADER and TITLE are
being put in these locations. It wouldn't be hard to add a "model title" as
well as "model name" and then use the title various places.
The problem I see with using COMPND is that it is really a list of
components that could be in any order. That "2" in "COMPND 2" is just a
continuation line marker, so that's not reliable, and it isn't represented
by anything in the CIF file. For example, for 1hje we have:
CIF:
_struct.entry_id 1HJE
_struct.title 'CRYSTAL STRUCTURE OF ALPHA-CONOTOXIN SI'
_struct.pdbx_descriptor 'ALPHA-CONOTOXIN SI'
_struct_keywords.entry_id 1HJE
_struct_keywords.pdbx_keywords CONOTOXIN
_struct_keywords.text 'CONOTOXIN, NICOTINIC ACETYLCHOLINE
RECEPTOR, TOXIN, VENOM'
PDB:
HEADER CONOTOXIN 15-JAN-01 1HJE
TITLE CRYSTAL STRUCTURE OF ALPHA-CONOTOXIN SI
CIF:
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.details
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.pdbx_ec
1 polymer syn 'ALPHA-CONOTOXIN SI' 1359.654 1 'AMIDATED C-TERMINUS' ?
'RESIDUES 50-62' ?
2 water nat water 18.015 27 ? ? ?
?
loop_
_entity_name_com.entity_id
_entity_name_com.name
1 'SI (2-7,3-13)'
2 ?
and then in the PDB we have:
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-CONOTOXIN SI;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: SI (2-7,3-13);
COMPND 5 FRAGMENT: RESIDUES 50-62;
COMPND 6 OTHER_DETAILS: AMIDATED C-TERMINUS
Does this help?
Bob
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2007-02-10 08:52
Message:
Logged In: YES
user_id=1082841
Originator: NO
whatever we do for PDB we should do for CIF or at least mmCIF
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1656702&group_id=23629
-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
