Hi Jinyao,
your question is not very well defined. It is considerably easier for
me if you tell me exactly what you tried to get this to work, which I
imagine was more than simply running g_spacial once and selecting the
volume_slice representation in vmd. That said,
1. Can you view it as an isosurface? That is a simpler representation
to get working and so is a valuable test.
2. Did you try pushing the bar that moves the slicing plane up and down?
2b. Did you try changing the axis and then repeating #2, above?
3. Open the "colors" dialog and go to color scales. When you see the
volume slice as entirely one color, does that color correspond to full
strength or no signal?
4. With the color scale mentioned above, try changing the offset and
magnitude of the gradient and see if that has any effect.
5. What options did you use when you ran g_spatial?
Chris.
Message: 1
Date: Fri, 13 Feb 2009 16:43:14 +0800
From: "Jinyao Wang" <[email protected]>
Subject: [gmx-users] how to get a solvent density map using
volumeslice in VMD
To: "gmx-users" <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="gb2312"
Hi gmx-users,
I want to get a solvent density map like that in the link
http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp
So I use g_spatial to calculate the spatial distribution function and
get a *.cube file.
I load the *.cube file into VMD and view it as an volumeslice but no
anything is displayed.
how can I get the solvent density map? If you have some
experience,please give me some suggestion.
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