[Chimera-users] [EXT] Re: spheres chimera

[Galotto, Giulia]

Thank you so much!

Best,
Giulia
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, March 19, 2020 11:58 AM
To: Galotto, Giulia <ggalotto at wpi.edu>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [EXT] Re: spheres chimera

On Mar 19, 2020, at 8:46 AM, Galotto, Giulia <ggalotto at wpi.edu<mailto:ggalotto at wpi.edu>> wrote:

Elaine,
I tried emailing the address you gave me and it gives me an error, it says that email does not exists.
I am sorry to bother you again, I would be happy to email the right address next time 🙂

In the mean time I will write here the problem I was having, feel free to forward it to the chimera address:

I clip the protein I am trying to visualize and I can actually see it sliced.
When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped.
I tried from both mac and pc. Do you have any idea why that might be?

Thank you so much for being so responsive to these emails! This is very helpful.

The email address chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>  definitely exists.   I cc'd it on this message and on the previous message.  It may say that you have to wait for the moderator to approve your message, but that usually happens in a day or two.  This is the best way to ensure you get an answer.

I cannot reproduce this problem.  When I clip the protein shown as spheres, for example using the Side View tool, the conic result shows the same clipping except with solid spheres.  See attached screenshot.

Elaine

[cid:8B1E6603-06D2-431D-9CD3-78E46DF06722 at gateway.sonic.net]



From: Galotto, Giulia <ggalotto at wpi.edu<mailto:ggalotto at wpi.edu>>
Sent: Thursday, March 19, 2020 11:41 AM
To: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [EXT] Re: spheres chimera

Hi all,
I have a question about the conic function.
I clip the protein I am trying to visualize and I can actually see it sliced.
When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped.
I tried from both mac and pc. Do you have any idea why that might be?

Thank you so much for being so responsive to these emails! This is very helpful.

Best,
Giulia
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, March 18, 2020 6:39 PM
To: Galotto, Giulia <ggalotto at wpi.edu>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [EXT] Re: spheres chimera

Hi Giulia,
(For next time), please send questions to chimera-users at cgl.ucsf.edu instead of me individually. I CC'd that address here.

There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces.

However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped.  You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is:

conic -o ~/Desktop/myfile.png -s

... which will then draw a non-movable image of the current position and create the specified output file.  There are other options to this command, see these pages for details:
<https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fconic.html&data=02%7C01%7Cggalotto%40wpi.edu%7Cc2ab23bc2fc140023ce508d7cb8d42c5%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637201679888328160&sdata=vsQvGS3QTQK7VQT5FbpTHL4LBdr%2FMmyditVvK2F2PRc%3D&reserved=0>
<https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fconic1.html&data=02%7C01%7Cggalotto%40wpi.edu%7Cc2ab23bc2fc140023ce508d7cb8d42c5%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637201679888328160&sdata=corNWpSxQtAjahAvKX9GU0NwIelZuosj85EaUW6ae8U%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto at wpi.edu> wrote:
>
> Hi,
> I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead.
> Is there a way to do this?
> Thank you so much!
> Best,
> Giulia Galotto
> Worcester Polytechnic Institute

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