Re: [Jmol-users] Problem with display of pdb file

[Inbal Tuvi-A. <in...@op...>]

Hello again,
 Thank you for the quick answers.  I believe the pdb file is written
correctly - it is a complex with Mo as the central atom, connected to 4
oxygen atoms and 2 nitrogen atoms.  In Jmol 10.0 I do not see the bond
between Mo and one of the nitrogen atoms, and the bond between Mo and
one oxygen atoms is also missing.  I do not have Rasmol, but I checked
it with Gaussian View and it looks just fine there.  I will try to
upgrade Jmol as suggested.
By the way, CONQUEST can create various types of molecular files, but I
need pdb files for the application I'm working on.

Best regards,
Inbal
 =20

-----Original Message-----
From: jmo...@li...
[mailto:jmo...@li...] On Behalf Of Bob
Hanson
Sent: Wednesday, June 28, 2006 3:42 PM
To: jmo...@li...
Subject: Re: [Jmol-users] Problem with display of pdb file


Inbal,

you should contact the makers of CONQUEST and tell them that they are=20
not writing proper PDB files.
They are putting too many connections on the CONECT lines. Specifically,

CONECT    1    4    5    6   14   15   16

indicates two hydrogen bonds -- to atoms 15 and 16.
This is what Jmol is displaying.

If you want to get around this, add the following script to your load=20
command:

connect (*) (*) single modify;wireframe 0.15

which says, "connect as a single bond any bond that already exists, and=20
display all bonds at the default bond size"

Alternatively, what other output formats does CONQUEST have? I just=20
wrote a Tripos SYBYL mol2 reader for 10.x.16. You could try that
instead.

Bob Hanson


Inbal Tuvi-Arad wrote:

>Hello to all,
>  I have a problem with the way Jmol displays pdb files and hope
someone
>can help me.  I downloaded a pdb file from the CSD.  When I open it in
>Jmol I can not see all the chemical bonds and some of the atoms are
>disconnected.  When I open it in Chime, or other chemical software I
can
>see all the bonds.  What could be the reason?
>
>Following is a copy of the file.
>
>Sincerely,
>Inbal Tuvi-Arad
>__________________________________
>Dr. Inbal Tuvi-Arad
>Department of Natural Sciences
>The Open University of Israel
>108 Ravutski St., POB 808,=20
>Raanana, 43107, Israel
>Tel: 972-9-778-1773
>Fax: 972-9-778-0661
>Email: in...@op...
>__________________________________
>
>HEADER    CSD ENTRY ADASMO
>COMPND    UNNAMED
>AUTHOR    GENERATED BY CONQUEST
>CRYST1   10.533   18.217   10.817  90.00 103.08  90.00 P 21/c        2
>CONECT    1    4    5    6   14   15   16
> =20
>


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