Feature Requests item #1656702, was opened at 2007-02-10 14:19
Message generated for change (Comment added) made by aherraez
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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.
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>Comment By: Angel Herraez (aherraez)
Date: 2007-02-13 17:24
Message:
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OK, what is being used for PDB files is completely reasonable. It seems
that I was was misguided by doing my testing with PDB files that have the
first line truncated or otherwise manipulated, so the filename is being
used for lack of a proper field at columns 63-66.
It could be a nice addition to have Jmol use the content of the following
columns too (say, from 63 to 72), since they are not given any use by the
official format --that will give space to put a longer name manually in
the file when it has been modified from the original pdb.
Apart from that, I think you shouldn't change anything. Sorry!
Regarding CIF and mmCIF, I am not familiar with those formats, but giving
the equivalent info looks the thing to do.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2007-02-13 16:58
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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 15:52
Message:
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whatever we do for PDB we should do for CIF or at least mmCIF
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