[Chimera-users] Questions about the electric fieldline
meng at cgl.ucsf.edu
Fri Dec 7 13:06:55 PST 2018
Hi Qiao Xue,
That is the SAME command as I said looked fine before (of course, you have to give the correct model number). I can only guess that the dx file is empty or wrong format or has weird values in it. For example, the potential could be ridiculously negative if you deleted all the hydrogens from the structure, or all zero if none of the atoms were assigned charges.
If you just open the example potential file 3eebB.phi in the tutorial linked below, for example, then that command (with model #0 if you opened 3eebB.phi as model #0) gives a bunch of pink lines.
Before bothering to try to show field lines, why don’t you display the molecular surface of the structure, color the molecular surface by this potential to see if it looks reasonable, using Electrostatic Surface Coloring (Tools.... Surface/Binding Analysis, see also tutorial).
Or, without coloring you could just look at the range of the dx file’s values in Volume Viewer (Tools… Volume Data… Volume Viewer, will automatically contain the dx values if you have opened the dx file) but that may be harder to interpret. You would expect both positive and negative values with peak near zero.
I hope this helps,
> On Dec 6, 2018, at 6:22 PM, xmgign at 126.com wrote:
> Hi Elaine,
> Thanks for your help.
> I have changed the model and now it works. The .dx file is #1.
> So I use the command: measure fieldLines #1 lines 500 startAbove 10 color pink linewidth 2.
> The command works but the field lines do not appear.
> Is there any problem of the commands?
> Qiao Xue
> xmgign at 126.com
> From: Elaine Meng
> Date: 2018-12-07 00:23
> To: xmgign at 126.com
> CC: chimera-users
> Subject: Re: [Chimera-users] Questions about the electric fieldline
> Hi Qiao Xue,
> Your command looks OK to me, but are you sure that the dx file is model #0? Check in the Model Panel (open from Favorites menu) that it is really model #0. If you have other things open at the same time, like the atomic structure, it could be #1, #2, etc. instead and you should change the model number in the command. Other than that, my only other idea is that the dx file is empty or the wrong format.
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Dec 5, 2018, at 11:52 PM, xmgign at 126.com wrote:
> > Hi
> > I want to make the electric fieldline but there are always some problems.
> > I did this as follows,
> > 1. run add charge to the system
> > 2. run APBS, the I get the electrostatic surface and a file named 1.dx
> > 3. open 1.dx
> > 4.measure fieldLines #0 lines 500 startAbove 10 color pink linewidth 2
> > then I get the problem : no volume specified
> > I have check the userguide of measure fieldlines, but there is nothing about the volume.
> > measure fieldLines map-model(s) [ lines N ] [ startAbove cutoff ] [ step s ] [ modelId model-number ] [ color line-color ] [ lineWidth width ] [ tubeRadius radius ] [ circleSubdivisions M ] [ markers true|false ]
> > what should I do next?
> > Thanks.
> > Qiao Xue
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