The HowTo Topic

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chuebsch
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The HowTo Topic

Post by chuebsch » 15 Nov 2009, 23:23

Hi, there!

Here, I am going to post some howto's for some features of MoleCoolQt.
But, if you have a question, feel free to post it here. :wave:

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Visualize Dipoles

Post by chuebsch » 15 Nov 2009, 23:54

After loading a structure it is possible to load one or more dipole vectors from a file via this button:
dipole.png
or via menu-file-Load Dipole moments [D].
The dipole moments file is a text file and it could look like this for example:

Code: Select all

Any text in the file will be ignored.
Theory: 10.0 3.0 -0.5 Any three numbers in a line are accepted as x,y and z of the dipole.
x 10.4 y2.970 z -0.773 
10.98(15) 3.102(3) 0.0(4) uncertainties in () are ignored.
11.98(15) 2.802(3) 0.1(4) color="green" you can specify a color like this. 
9.9(5) 2.0(3) -0.9(4) color="#fac0ed" or like this as in html.
x 10.4 y2.970 z -0.773 ## 0.5 0.3 0.0 this is also ok.
but the following is NOT!!!
9.9(5) 2.0(3) -0.9(4)  ## 0.5 0.3 1.0
if you want to remove the dipoles from the view you click on this button:
nodipole.png
Thats it so far. :colors: :color:
The length of the vectors is as if they are given in Angstrom.
If no color is specified MoleCoolQt assigns one.
Cheers
Christian
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peaks and holes or critical points with xd.res

Post by chuebsch » 16 Nov 2009, 00:23

Question: How can I show residual density peaks and holes of my XD refinement?
Answer: Just run 'xdfft' after that there should be a file called 'xd_fft.out' in the directory where your xd.res and xd.mas resides.
If you load now xd.res from that directory in MoleCoolQt, then peaks and holes will be shown.


Question: How can I show critical points from my XD refinement?
Answer:
Put a * before rho in your xd. mas file and uncomment the CPSEARCH line. Like for example here:

Code: Select all

PROPERTY core valence *rho defden gradrho d2rho esp nucpot sigrho siglap ef efg elf
...
...
...
CPSEARCH bond rmin  0.9 rmax  1.7
Run 'xdprop' and then there should be a file called 'xd_rho.cps' in the directory of xd.mas and xd.res. If you load now xd.res from that directory in MoleCoolQt, then critical points will be shown.

Cheers
Christian

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Re: The HowTo Topic

Post by chuebsch » 16 Nov 2009, 15:12

OK, here are some basic questions.
Question: How can I zoom into my structure?
Answer: Just press the right mouse button and move up or down. The [page-up] and [page-down] keys do the same.

Question: How can I change the size of the Labels?
Answer: Just scroll with your mouse, or press '+' / '-' on the keyboard.

Question: How can I rotate the molecule?
Answer: Just press the left mouse button and move around, ore use the arrow keys of your keyboard.

Question: How can I move the structure around?
Answer: Just press the middle mouse button and move around.
[Ctrl] + arrow keys do the same if you wish.

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The Filter Dialog

Post by chuebsch » 17 Nov 2009, 12:31

Question: How can I weed out Dummy atoms?
Question: How can I weed out (Q-)peaks and holes?
Question: How can I weed out critical points?
Answer: Use the filter dialog.
filter.png
filter1.jpg
Change the check box to 'Atomic number' and then press OK.
Because the starting value is 0 by default. All non natural atoms are weeded out.
Here are the atomic numbers for some objects:
  • PK /HL: -3
  • CP: -2
  • DUM0: -1
Of course there are more ways to do that. You could for example type "C|N|O|F" into the
Pattern field to see only carbon, nitrogen, oxygen and fluorine atoms.
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