[Jmol-users] Re: Jmol too nice behaviour

[Miguel H. <mt...@mt...>]

Miguel & Jaim wrote:

> Please send me the entire file so that I can look at it.

You indicated that the entire file was what was in your original message.
I have included it below for reference purposes

>> We find out that we're sending some incorrect data to Jmol,
>> like a CONNECT with a non-existing atom name (see the example
>> at the end).

Yes, I see some 'extra' references.

>> It turns out that Jmol is too nice with us and draws something.
>> Since some of the conections are incorrect, I assume that the
>> generated structure is not correct, but I had no other way of
>> knowing about the incorrect data.
>
> That is *not* good.

I misunderstood your original message ...

>> We hope to fix the data soon, but I think is interesting to
>> know what's the default behaviour of Jmol.
>>
>> Shall Jmol ignore errors and try to draw what's available?

Yes, Jmol ignores file errors and makes a 'best efforts' attempt to draw
whatever is in the file that is presented.

Many people want to do things like cut out pieces of a .pdb file in order
to show the structure. Therefore, extra references to atoms are ignored.

> Clearly there is a bug in Jmol. It should not generate an image that is
> incorrect.

I thought that you were saying that Jmol was creating bonds where none
existed. That is not the case.

Jmol's rendering of the file below *is* correct. It has rendered exactly
what you gave it. If the structure does not make sense chemically then you
need to use another type of tool for structure verification.


>> Shall Jmol report errors somehow and stop?
>
> Unfortunately, *many* files have errors. I do not think that Jmol should
> stop ... other many people will never see anything :-)

When errors are encountered Jmol does its best to keep moving and to
display what it can.

> But it should not draw bonds where none exist ... that is a bug.

Jmol has not added any extra bonds to the file below. It draws what you
gave it.

Jmol does no checking to determine whether or not something makes sense
chemically. An atom can have dozens of bonds with arbitrary lengths and
Jmol will happily render it.


Miguel

------------------

HEADER
HEAD  LIGAND  FS4
HETATM 5763 FE1  FS4 A 733       0.671  35.798 101.733
HETATM 5764 FE2  FS4 A 733       1.708  33.346 101.586
HETATM 5765 FE3  FS4 A 733       2.845  35.141 103.255
HETATM 5766 FE4  FS4 A 733       3.166  35.443 100.573
CONECT 5763 4035 5764 5765 5766
CONECT 5763 5767 5768 5769
CONECT 5764 4125 5763 5765 5766
CONECT 5764 5767 5768 5770
CONECT 5765 4198 5763 5764 5766
CONECT 5765 5768 5769 5770
CONECT 5766 4057 5763 5764 5765
CONECT 5766 5767 5769 5770
CONECT 5767 5763 5764 5766
CONECT 5768 5763 5764 5765
CONECT 5769 5763 5765 5766
CONECT 5770 5764 5765 5766
END