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Re: Low-quality NCI despite high quality grid

dummy@example.com (saeed_E) — Tue, 31 Dec 2024 06:21:18 +0000

Dear Tian,
Many many thanks for your highly kind attention. While you stated that "you have sent it to me", I cannot find this chapter in my mail box. If possible, please send me again this so nice chapter.

Sincerely,
Saeed

Re: Low-quality NCI despite high quality grid

dummy@example.com (sobereva) — Tue, 31 Dec 2024 04:39:49 +0000

saeed_E wrote:

Dear Tian,
Unfortunately, our university has no access to the Elsevier publications. Could you please send me a copy of your so informative publication " http://dx.doi.org/10.1016/B978-0-12-821978-2.00076-3" through my email address?
Sincerely,
Saeed

I have sent it to your E-mail

Anyone needs the article "Visualization Analysis of Weak Interactions in Chemical Systems" can also send E-mail to me to request.

Re: Low-quality NCI despite high quality grid

dummy@example.com (saeed_E) — Tue, 31 Dec 2024 03:24:24 +0000

Dear Tian,
Unfortunately, our university has no access to the Elsevier publications. Could you please send me a copy of your so informative publication " http://dx.doi.org/10.1016/B978-0-12-821978-2.00076-3" through my email address?

Sincerely,
Saeed

Re: Low-quality NCI despite high quality grid

dummy@example.com (sobereva) — Mon, 30 Dec 2024 18:52:51 +0000

I never use Chimera to plot this kind of map. The graphical effect of VMD is already satisfactory enough.

Re: Low-quality NCI despite high quality grid

dummy@example.com (andrzejek) — Mon, 30 Dec 2024 16:45:51 +0000

Thank you. Will check that out.
How about plotting such graphic in Chimera (not ChimeraX). Do you have a working formula for that?
Best

Re: Low-quality NCI despite high quality grid

dummy@example.com (sobereva) — Mon, 30 Dec 2024 16:23:03 +0000

The "high quality grid" is named for relatively small systems. For large systems, you should manually input a grid spacing in the option "4 Input the number of points or grid spacing in X,Y,Z, covering whole system". Grid spacing of 0.15 Bohr can result in relatively smooth isosurfaces, using 0.08 Bohr can obtain perfect isosurfaces while the cost is generally fairly high.

The importance of grid spacing has also been mentioned in my review article about visual analysis of weak interactions:
Tian Lu and Qinxue Chen, Visualization Analysis of Weak Interactions in Chemical Systems. In Comprehensive Computational Chemistry, vol. 2, pp. 240-264. Oxford: Elsevier (2024) http://dx.doi.org/10.1016/B978-0-12-821978-2.00076-3

Low-quality NCI despite high quality grid

dummy@example.com (andrzejek) — Mon, 30 Dec 2024 10:34:32 +0000

Dear All,

I am generating an NCI graphic using Multiwfn with the following input:

Multiwfn orca-optimized.molden.input << EOF
20
1
3
3
2
EOF

Despite selecting the high-quality grid option (option 3), the output appears to be of low quality:

Could anyone provide guidance on resolving this issue?

// Also, maybe there's an option to generate such in Chimera instead of VMD?

Thank you