[Chimera-users] adding dashed lines, showing transparent spheres

[Thirumurugan Prakasam]

Hi,
I need help to stack the crystal structures stack on top of each other. For
your understanding, I have just shown the image below something like that I
wanted to make. Would you please help me with how to make stacked molecular
structures using chimera?
[image: image.png]

Thanks,
Thiru


On Mon, Feb 24, 2020 at 10:31 PM Thirumurugan Prakasam <tp42 at nyu.edu> wrote:

> Thank you soo much for your update and support. I will try.
> Thanks
> Thiru
>
> On Monday, February 24, 2020, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Thiru,
> > (I added a subject line to the message so others may be able to find it
> later.)
> >
> > (A) There are a couple ways to add a dashed or dotted line, but one easy
> way if you only need to add a few is to first just make distance
> measurements, and then hide the distance values.  For example, show
> Distances tool (menu: Tools… Structure Analysis… Distances).  Then for each
> line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second
> atom to select it …. now there are two atoms selected and you can add the
> line between them by clicking the “Create” button on the Distances tool.
> >
> > With the Distances tool you can set “Labels” to “None” and change the
> distance color, line width, and line style.
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_structuremeas_structuremeas.html-23distances&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=mTaIq5duDt2KEUvjZ22s7x2ef0JCMbb5qxd6N99pbLQ&e=
> >
> >
> > You should do this when only one copy of the structure is open, and
> shown as sticks.  Part (B) below   describes opening a second copy to show
> the spheres, and if you do that first, you will have to use Model Panel to
> hide the spheres model temporarily (uncheck the “S” box) so that you can
> add the distance measurements to the sticks.
> >
> > (B) To show transparent spheres and sticks at the same time, open the
> same structure twice.  Then show one copy as spheres and make it partially
> transparent.  For example, commands:
> >
> > open pubchem:448537
> > open pubchem:448537
> > repr sphere #1
> > trans 50 #1
> > set bg_color white
> >
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_represent.html&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=ATsOk1_wSRwAMqCIwFex8WeDxbwIx2hXCOEbm2efLPA&e=
> >
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_transparency.html&d=DwIFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=GE3ZfZWTV3qAQwbrb_Dh9Jc4z3-xDklkVZTf8IQl1c4&s=6aGA_PyYN5-BQKjot6hrZUgL7uS9BoYcdlsAvJt0Xw8&e=
> >
> >
> > The 50 means 50% transparent.  You could use some other value.  Also you
> could change the colors of the spheres (model #1 in this example) and
> sticks (model #0 in this example) as you like.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam <tp42 at nyu.edu>
> wrote:
> >>
> >> Hi,
> >> I am trying to make metal coordination bond as a dotted line and also I
> need to make electron clouds around the atoms as in the picture below
> (Please provide me short guidelines on how to make nice cartoon). Please
> help me sort this two issues.
> >> Looking forward to hearing from you,
> >> Many thanks,
> >> Thiru
> >> <image.png>
> >>
> >> _______________________________________________
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> >
> >
>
> --
> Thirumurugan Prakasam,
> Research Scientist,
> New York University Abu Dhabi,
> Experimental Research Building
> Building C1, Saadiyat Island
> Abu Dhabi, UAE
> Phone no: +971-561976358
>
>
>
>

-- 
Thirumurugan Prakasam,
Research Scientist,
New York University Abu Dhabi,
Experimental Research Building
Building C1, Saadiyat Island
Abu Dhabi, UAE
Phone no: +971-561976358
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