Subject: Re: CCL:Adding H-atoms??

From: <[email-masked]>
Date: Wed, 8 May 96 10:28:52 EDT

[following up to my own message...]
>>  For example, one can convert crystallographic xyz coordinates into
>>ALCHEMY input with BABEL.  But this conversion involves looking at
>>the "bonding nature" of the atoms and doesn't seem to work if the
>>hydrogen atoms are missing.
>
>This is a deficiency of Babel, not Alchemy.

I have had two people attack me for making this statement, and it's still 
early morning.  Sigh.  Let me try again:

"If true, this is a deficiency of Babel, not Alchemy"

Does that make everyone happy?  The original poster seemed like a fairly
intelligent fellow who made a good effort to solve his own problem before
posting to this list.  From his post, I thought it reasonable to assume 
that he had attempted several of the more-obvious solutions, including
changing the conversion parameters within Babel.  I have not had extensive
experience with Babel, so I took his word for it.

I find it somewhat disappointing that neither of the people who saw fit to 
criticize me have decided themselves to post any information that would 
actually help the original poster.  (At least, nothing has reached me yet.
The way things are going, their posts and this post will cross in the ether.)

So chill out, folks!

Jonathan Brecher
CambridgeSoft Corporation
[email-masked]

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From: David Larson <[email-masked]>
Date: Wed, 8 May 1996 10:50:42 -0500 (CDT)

Alchemy will import crystal coordinate data using the File >> Crystal...
command.  The file format can be found on p91 of the the Alchemy manual.
Another alternative is to convert it to pdb format and then import it into
Alchemy.

If you have any questions or problems please let me know.

Cheers,
Dave

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David Larson					Email:  [email-masked]
Customer Support Scientist			Phone:  314 647 1099
TRIPOS Inc					FAX:    314 647 9241
St Louis MO 63144
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From: "William T. Winter" <[email-masked]>
Date: Wed, 8 May 1996 21:54:33 -0400 (EDT)

On Tue, 7 May 1996 [email-masked] wrote:

> 
> >  I need to know how to add hydrogen atoms to a large crystallographic
> >structure that does not report the hydrogen atom positions.
> >  Programs like ALCHEMY have an "add H" option that is useful in
> >drawing structures, but I can't find a good way to get the coordinates
> >into ALCHEMY.
This request seems a little odd since Alchemy has a "crystal input" option
Using it is fairly simple, you need the unit cell parameters, found in 
the abstract and again in a small table, in any standard crystal 
structure report.   then you need the coordinates, and you have to change 
the namesd of the atoms from those given in the paper to atom types 
recognized by alchemy.  These are listed in the manual or if you do not 
have it they can be found in the file "atomdef.tab" in the "tables" 
directory.
Alchemy even includes a a sample of a crystal input file, it has the file 
extension ".cry".

Finally, you can also use the crystal input routine to input cartesian 
coordinates by setting the a=b=c=1.00 and alpha=beta=gamma=90.0 on the 
lattice constant card.  Once the structure is in you can then add 
hydrogens in alchemy.  This is also a convenient route into other 
modeling programs since alchemy can write mm2 and sybyl file structures.
  If you need other sample files I can provide them but not for peptides.
 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. William T. Winter                  Phone: (315)470-6876
315 Baker Lab                          FAX:   (315)470-6856
SUNY-ESF                               Internet: [email-masked]
Syracuse, NY 13210-2786                URL     http://www-chem.esf.edu