VMD-L Mailing List

From: Sebastian Reiter (Sebastian.Reiter_at_campus.lmu.de)
Date: Wed May 27 2020 - 09:36:37 CDT

Hello Francesco,

it still looks a bit strange in my opinion. An additional point you
could try is using a smaller isovalue to get a surface further away from
the nuclei. This will likely give you both a smoother surface and a more
expressive colormap for the ESP.  A nice demonstration of this can be
found on Felix Plasser's blog:
https://chemical-quantum-images.blogspot.com/2019/09/esp-with-different-isovalues.html

Best
Sebastian

Am 27.05.20 um 16:23 schrieb Francesco Pietra:
> Hallo Sebastian
> I have resumed my trials with plotting the electrostatic potential onto the
> eldens. Following your recipe, with Gaussian standard files for water I
> have now obtained a fully satisfactory image with values far from
> -0.15/+0.15 (attached screenshot, I forgot to add the skeleton)
>
> This is good starting point to understand whether the eldens/pot files
> (which do not obey the Gaussian standard, in fact can't be opened with
> MOLDEN) for my system are of low quality or my dealing with them was
> inadequate.
>
> thanks a lot
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, May 26, 2020 at 9:54 AM
> Subject: Re: Fwd: vmd-l: Fwd: Electrostatic potential maps
> To: Sebastian Reiter <Sebastian.Reiter_at_campus.lmu.de>, VMD Mailing List <
> vmd-l_at_ks.uiuc.edu>
>
>
> Hallo Sebastian
> With the last corrections (next to Volume mep.cube; next to Range
> eldens.cube), and having also loaded the.xyz file and using Transparency
> and Tachyon rendering, it works. However, by playing around -015/0.15 I
> could not do better than in the attached screenshot.
>
> I have used extensively VMD through the years, except for rendering images,
> so that I assume that I am not exploiting the VMD capabilities to this
> concern. Such a poor graphics, and colors far from representing the
> electrostatic potential, can't be due to a small grid.
>
> Thanks a lot for all your guidance
>
> francesco
>
>
> On Mon, May 25, 2020 at 6:45 PM Sebastian Reiter <
> Sebastian.Reiter_at_campus.lmu.de> wrote:
>
>> Hi Francesco,
>>
>> no worries, that's what the mailing list is for ;)
>>
>> The way you describe it, you're mapping the density onto the ESP, but
>> you actually need it the other way round. That means, next to "Volume"
>> you need to choose "mep.cube" and next to "Range" choose "eldens.cube".
>> Then, the color map should look right.
>>
>> Unfortunately, I have no experience with Chimera, but VMD has given me
>> excellent results in the past. You can also make the Isosurface
>> transparent (choose Material -> Transparent) and add another
>> representation for the molecular skeleton structure (Licorice is usually
>> a good choice). The transparency effect will look much nicer once you
>> render the scene with VMD's render engine Tachyon.
>>
>> Best
>> Sebastian
>>
>> Am 25.05.20 um 18:04 schrieb Francesco Pietra:
>>> Hallo Sebastian
>>> By playing a lot around -0.15 and +0.15 in the "Color Scale Data Range",
>> I
>>> could not do better than in the attached screenshot.
>>> In the "Draw style" window, for Coloring Method I choose "Volume" and
>> right
>>> to Volume, I choose eldens.cube.
>>> Right to "Range" I choose mep.cube.
>>>
>>> I am not mailing to VMD because I have another question. Did you try
>> these
>>> affairs with CHIMERA? For the same grid as here it has a perfect graphics
>>> and with transparency it allows visualizing the molecular skeletons. It
>>> also allows a good 3D. It only requires the mep.cube and I succeeded
>>> immediately in plotting the electrostatic potential on a surface with
>>> correct colors ( neat blue for high potential, neat red for low
>> potential).
>>> I did not take notice of the commands that I used and thereafter I am no
>>> more able to plot on the surface. Always the plot goes to the volume and
>>> therefore it does not accept colors.
>>>
>>> I can well imagine that your patience is exhausted. I can only thank you
>>> francesco
>>>
>>> On Mon, May 25, 2020 at 4:56 PM Sebastian Reiter <
>>> Sebastian.Reiter_at_campus.lmu.de> wrote:
>>>
>>>> Hi Francesco,
>>>>
>>>> glad it works now. You're almost there, just make sure the density cube
>>>> is selected in the dropdown menu for the Isosurface and try something
>>>> like -0.15 and 0.15 for the minimum and maximum of the color range. If
>>>> you want to improve the quality of the surface, you need to specify a
>>>> finer grid in the orca_plot and mep.py steps.
>>>>
>>>> Best
>>>> Sebastian
>>>>
>>>> Am 25.05.20 um 16:31 schrieb Francesco Pietra:
>>>>> Hi Sebastian
>>>>>
>>>>> Thanks for the detailed instructions.
>>>>>
>>>>> I already had most files, except the full SCF electron density in cube
>>>>> format that have now generated according to your recipe.
>>>>>
>>>>> As you can see from the attached screenshots, SELECTION succeeded,
>> except
>>>>> for the horrible graphics.
>>>>>
>>>>> With TRAJECTORY, I was unable to tune the color, in particular
>> obtaining
>>>> a
>>>>> single color, not the desired blue-white-red according to the charge
>>>>> distribution. I also tried color by charge but it did not work.
>>>>>
>>>>> I could not realize were I am wrong.
>>>>>
>> sd