Sebastian Lisken wrote:
> 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.
the RasMol 2.7.2.1 online help says:
Connect
Syntax: connect {<boolean>}
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. The command 'connect false'
uses a fast heuristic algorithm that is suitable for determining bonding in
large bio-molecules such as proteins and nucleic acids. The command 'connect
true' uses a slower more accurate algorithm based upon covalent radii that
is more suitable to small molecules containing inorganic elements or
strained rings. If no parameters are given, RasMol determines which
algorithm to use based on the number of atoms in the input file. Greater
than 255 atoms causes RasMol to use the faster implementation. This is the
method used to determine bonding, if necessary, when a molecule is first
read in using the 'load' command.
on load, RasMol uses the CONECT record stored in the PDB file, if there are none,
RasMol calculates the connection information.
make your own test with 1ndh
load pdb pdb1ndh.ent
restrict fad
# the connections look well
# and this is because of the CONECT records
# as you could demonstrate by:
save pdb fad.pdb
# look into the file, it lacks CONECT records
# this should be done better with Jmol :-)
load pdb fad.pdb
# the adenine ring looks really awful
# but this is a completely other RasMol bug
# and Jmol seams to suffer the same bug
# have you recognized that all ring atoms are pink
# there is a exception of the PDB file format with ?nearly? all these
# nucleotide derivate ligands as FAD NAD ... which should be
# http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_67.html
# COLUMNS 13 - 16 Atom name Atom name.
# where the element symbol should be right justified at position 14 and
# http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
# <<###
* Columns 77 - 78 contain the atom's element symbol (as given in the periodic table),
right-justified. This is especially needed
because in some cases it has not been possible to follow the convention that columns
13 - 14 of the atom name contain the element
symbol. The most common cases are:
- In large het groups it sometimes is not possible to follow the convention of
having the first two characters be the
chemical symbol and still use atom names that are meaningful to users. A example
is nicotinamide adenine dinucleotide,
atom names begin with an A or N, depending on which portion of the molecule they
appear in, e.g., AC6 or NC6, AN1 or
NN1.
- Hydrogen naming sometimes conflicts with IUPAC conventions. For example, a
hydrogen named HG11 in columns 13
- 16 is differentiated from a mercury atom by the element symbol in columns 77 -
78. Columns 13 - 16 present a unique
name for each atom.
###
# but there is no element symbol in 1ndh
# therefore the atom radii of Ac and An are used
cpk
cpk off
# and using "exact calculation" results in garbage while
connect false
# the heuristic, gives good results
# as is achieved if you edit 1ndh.pdb
# s/ A(...) FAD 273/ \1 FAD 273/g
# then the element type is recognized correctly
# and on loading (connect true) gives good results
Jmol should deal with these ligands as they are very common
and it should be possible to reset Jmol to the PDB files CONECT record information,
e.g.
set connect file
> Q: How do I tell if the CONECT records are for 'all' the bonds or only for
> the 'nonstandard' bonds?
>
use CONECT if present and calculate the rest
> 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?
>
don't know, I used
bond <number> <number> +
on an existing bond (or twice) to alter the wireframe representation
>
> 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?
>
connect [false|off|1.54]
calculate connections according to heuristic, e.g. assuming to deal with average C N O
bond length which may be less then e.g. 1.98 ?who knows?
I don't know if it is simply bond length which is used by RasMol heuristic, but if,
I'll suggest to allow, in addition to the parameters false or off, which RasMol uses,
to set the distance e.g. 1.54 which is said to be the average C-C or 1.10 for N%N
(nitrogen:-)
connect [true|on]
to use all information about an atom e.g. atom radius to calculate bonding
connect file
which resets to the state after file loading (uses CONECT records)
Regards, Jan
>
--
Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813.
Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i
mailto:[EMAIL PROTECTED]
-------------------------------------------------------
This SF.net email is sponsored by: SF.net Giveback Program.
Does SourceForge.net help you be more productive? Does it
help you create better code? SHARE THE LOVE, and help us help
YOU! Click Here: http://sourceforge.net/donate/
_______________________________________________
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users
