Hi again,
I hope I'm not just restating stuff, but the best explanation of the
CONECT handling routines in RasMol/Chime I am aware of is:
http://www.umass.edu/microbio/rasmol/rasbonds.htm
>From this, my understanding and experience is that the behaviour of
Rasmol/Chime is as follows:
Default RasMol/Chime behaviour
If the number of CONECT records >= the number of atoms (+ hetatoms) then
CONECT records are used for the bond display
If the number of CONECT records < the number of atoms (+ hetatoms) then
CONECT records are discarded and bonds are calculated by one of two
methods:
(1) a quick and simple method (optimised for biological
macromolecules) for connectivity for structures >255 atoms
(2) a more complex algorithm for structures <=255 atoms
connect false
forces the fast algorithm (1) for any structure
connect true
forces the more complex algorithm (2) for any structure
set connect true
is equivalent to the above default behaviour.
set connect false
(which must be issued before loading the PDB file) forces only the
CONECT records to be used and no bonds to be calculated
set connect save
(Chime 2 only - which must also be issued before loading the PDB file -
not well documented) both shows bonds in CONECT records and calculates
bonds not specified in CONECT records by the methods detailed above.
Personally, I am not too bothered if Jmol sticks precisely to the
Chime/Rasmol commands. As long as Jmol/JmolApplet allows for the above
options in a consistent, logical, and (where possible)
standards-compliant way I will be more than happy to edit any scripts
appropriately. It is important both to be able to render reasonable
'bonded' structures for biological macromolecules which lack (most)
CONECT records, and also accurately render structures where full CONECT
records are given.
Info on multiple bonds and CONECT records can be found at
http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds
I recollect that default behaviour for rendering multiple bonds may have
changed between RasMol 2.6 (detailed above) and OpenRasMol 2.7 - but I
have not checked this.
Regards
Geoff
Message: 10
Date: Tue, 18 Nov 2003 23:45:17 +0100 (CET)
From: "Miguel" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>,
<[EMAIL PROTECTED]>
Subject: [Jmol-users] CONECT .pdb questions
Some .pdb files have CONECT records. Jmol currently ignores them.
I have read the PDB file format specification
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
and have looked at some .pdb files ... and I am a little confused about
what I should do.
It looks like to me that the spec says that CONECT records are used for
special cases. The implication is that CONECT records are not needed
within standard residues. And in fact, many .pdb files have relatively
few CONECT records ... so that seems consistent to me.
That seems to imply that (in this case) Jmol should build its own
bonds and add the CONECT bonds.
But I have seen other .pdb files which *do* seem to have all the CONECT
records there. And, in general, Jmol will not calculate bond
connectivity information if this information is in the file.
In this case, Jmol should *only* use the connectivity specified in the
CONECT records.
Q: How do I tell if the CONECT records are for 'all' the bonds or only
for
the 'nonstandard' bonds?
Q: It seems I recall seeing something about a format 'extension' where a
CONECT record could be specified more than once in order to define a
double/triple bond. Is that true?
Another factor ... the RasMol documentation for the 'connect' command
says:
The RasMol 'connect' command is used to force RasMol to
(re)calculate the connectivity of the current molecule.
If the original input file contained connectivity
information, this is discarded.
So, that doesn't seem right to me in the case where a file is following
the PDB format specification and standard connectivity is not included
in
the CONECT records.
Q: What should the connect command do?
Miguel
--__--__--
Message: 11
Date: Tue, 18 Nov 2003 23:59:09 +0100
From: Sebastian Lisken <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: [Jmol-users] Re: CONECT .pdb questions
I'm certainly not an expert on CONECT in .pdb, but in my experience
CONECT has exactly that problem. When we introduced Rasmol as a viewer
into our CaGe program, I looked into "set connect" as a possible
means of making Rasmol follow the connection information in the
file exactly. I remember reading in some manual and deciding that
"set connect" would not do that for me. Colleagues that were using
Rasmol for a long time (in the previous version of CaGe) always said
there was no way of "taming" Rasmol. As a result, we only run
Rasmol after displaying a warning to the user. When people on the
list wrote about their interpretation of "set connect", it seemed
like the meaning I would have wanted for the command, but I didn't
take the time to check up on this, so I didn't comment.
If you're after connectivity, I guess you'll have to investigate
precisely what "set connect" does and does not do. My idea is that
whatever you do with "set connect", there is always some chemical
interpretation of the data taking place, and I gave up on trying
to understand or influence that algorithm. That's one of two
reasons why I want Jmol's CML reader to accept a "MathGraph"
molecule convention. (The other reason was that I can pass CML
data in an applet parameter, whereas PDB data could only be passed
through a file in Jmol 0.6.1.)
Sebastian
--__--__--
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