[Chimera-users] Chimera-users Digest, Vol 193, Issue 5
Boaz Shaanan
bshaanan at bgu.ac.il
Sun May 5 05:27:35 PDT 2019
Hi Again,
Following my complaint on the cube format I started to play with .dx format of APBS which so far seems more promising in how it projects on the protein surface.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of chimera-users-request at cgl.ucsf.edu <chimera-users-request at cgl.ucsf.edu>
Sent: Sunday, May 5, 2019 8:18 AM
To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 193, Issue 5
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Today's Topics:
1. save sequence alignment (Hernando J Sosa)
2. Re: save sequence alignment (Eric Pettersen)
3. Re: RR distance map, scale normalization (Arvind SHARMA)
4. Handling electrostatic potential in cube format (Boaz Shaanan)
5. How to select residues/atoms only those within my cryo-EM map
region (Kim, Doo Nam)
----------------------------------------------------------------------
Message: 1
Date: Fri, 3 May 2019 21:03:33 +0000
From: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
To: Chimera <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] save sequence alignment
Message-ID:
<F0E461AAE34D0448B6EE7D31E433B7080154B87577 at AEWEXCPM21.yuad.uds.yu.edu>
Content-Type: text/plain; charset="utf-8"
Dear Chimera,
Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script?
Thanks
H.
------------------------------
Message: 2
Date: Fri, 3 May 2019 15:19:36 -0700
From: Eric Pettersen <pett at cgl.ucsf.edu>
To: Hernando J Sosa <hernando.sosa at einstein.yu.edu>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] save sequence alignment
Message-ID: <EFACEFC8-FD06-4C10-AE7B-704CD8925BCF at cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
Hi Hernando,
This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can?t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course.
Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory.
?Eric
Eric Pettersen
UCSF Computer Graphics Lab
> On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
>
> Dear Chimera,
>
> Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script?
>
> Thanks
>
> H.
>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 3
Date: Fri, 3 May 2019 23:44:47 +0000
From: "Arvind SHARMA" <arvind.sharma at pasteur.fr>
To: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] RR distance map, scale normalization
Message-ID: <77099411f94743339d9ed58d02f06ad2 at pasteur.fr>
Content-Type: text/plain; charset="windows-1252"
Thanks for your reply Elaine.
Have a nice weekend
Arvind.
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, May 3, 2019 4:19:39 PM
To: Arvind SHARMA
Cc: Chimera User Help
Subject: Re: [Chimera-users] RR distance map, scale normalization
Hi Arvind,
Unfortunately not, it is a limitation of RR distance maps. It is mentioned in the technical notes section at the bottom of the page, "Coloring is applied across the full value range.?
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html>
Sorry about that,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On May 3, 2019, at 12:11 AM, Arvind SHARMA <arvind.sharma at pasteur.fr> wrote:
>
> Hi,
>
> I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white.
>
> Thanks.
> Best wishes,
> Arvind.
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Message: 4
Date: Sat, 4 May 2019 21:51:23 +0000
From: Boaz Shaanan <bshaanan at bgu.ac.il>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Handling electrostatic potential in cube
format
Message-ID: <6cd849c030d847f4a1d5e86d39cfdf5d at bgu.ac.il>
Content-Type: text/plain; charset="iso-8859-8-i"
Hi,
It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues.
Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version.
Thanks for your help.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
------------------------------
Message: 5
Date: Sun, 5 May 2019 05:17:47 +0000
From: "Kim, Doo Nam" <doonam at lanl.gov>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] How to select residues/atoms only those
within my cryo-EM map region
Message-ID: <b1d7055b52cf4145b72a567141ccefc8 at lanl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
I want to select residues/atoms only those within my cryo-EM map region so that I can highlight/color them.
As I googled ("select atoms only within a map chimera"), I could find only how to select residues/atoms within certain radius from specific position/atoms.
I may use phenix.map_model_cc to see which residues have higher cc to my cryo-EM map and manually select those using a script.
However, I'm just curious whether there is already a good automatic chimera function that I can use to select residues/atoms only those within my cryo-EM map region.
best,
Doonam
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