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Re: [Bkchem-user] Hydrogen labels and \n for new lines

From: Robert Funnell
Subject: Re: [Bkchem-user] Hydrogen labels and \n for new lines
Date: Mon, 18 May 2009 07:53:33 -0400 (Eastern Daylight Time)
User-agent: Alpine 2.00 (WNT 1167 2008-08-23)

Beda -

On Mon, 18 May 2009, Beda Kosata wrote:

Robert Funnell wrote:
I just discovered BKchem yesterday and I like it. I had some
difficulty getting started with the documentation that I found, so I
created a little Web page to remind me of what I've learned. FWIW,
it's at http://audilab.bmed.mcgill.ca/~funnell/swil_bkchem.html.
I hope that it's accurate as far as it goes.

Thanks. The documentation is very old and I did not update it for ages.

I must confess that it was only after figuring things out and writing my Web page that I discovered that a user's manual is included in the distribution. Unless I missed something, perhaps a line (e.g., 'A user's manual included in the doc/ directory of the installed files') could be added to the Web site (e.g., on the Install page)?

Any new piece of information available to the users is welcome.

I've taken the liberty of adding a link to the wiki howtos page, as well as a mention of the user's manual.

As noted on that page, I ran across a couple of problems.

One is that I couldn't get BKchem to not display the labels of
hydrogen atoms once I'd specified them as hydrogen. Is that what the
Options > Standard > Atom setting is supposed to do?

This dialog is for global settings - it influences only new drawings
(unless you select to apply it to existing items in the lower part of
the dialog).
To make changes in existing items, you can either use the context menu
(right-click) and select "Hydrogens->Off" or "Properties->Hydrogens->Off".

I did select to apply it to the whole drawing and to existing values, and I've also right-clicked and selected Hydrogens->Off, but nothing seems to change. The H's are still displayed. Perhaps I'm missing the point. What I expected was that I could explicitly label atoms as H, and then have those H's be either visible or not visible. Is that the way it's supposed to work?

- Robert

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