[Chimera-users] Volume Eraser
Tom Goddard
goddard at sonic.net
Thu Dec 12 10:07:08 PST 2019
Hi Wangbiao,
The problem is your map values are all negative and volue eraser replaces the values with zero which is then the largest value in the map. First make a copy of your map with positive values by shifting by 50000 or by scaling by -1 with the vop scale command and use volume eraser on that map.
Tom
> On Dec 12, 2019, at 6:27 AM, Guo, Wangbiao <wangbiao.guo at yale.edu> wrote:
>
> Dear all:
> I use the chimera (chimera-alpha-mac64) and input the room temperature FIB data (.mrc file), which is a huge algae cell (see below). I want to delete some map area, and used the Volume Eraser. But it can not delete but increase map. Is there any one knows how to fix it? I attached my screen record.
>
>
> Seven Guo
> <Screen Shot 2019-12-12 at 9.22.13 AM.png>
>
> > On Dec 11, 2019, at 1:25 PM, chimera-users-request at cgl.ucsf.edu wrote:
> >
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> > Today's Topics:
> >
> > 1. Re: ViewDock not showing results (Don Gabo)
> > 2. Conference Announcement: Molecular Modeling Workshop, Feb
> > 17-19, 2020 in Erlangen, Germany (Harald Lanig)
> > 3. selection of specific bonds (Damien Larivi?re)
> > 4. Re: selection of specific bonds (Elaine Meng)
> > 5. Re: selection of specific bonds (Eric Pettersen)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 9 Dec 2019 13:10:30 -0600
> > From: Don Gabo <gabrielsrbio at gmail.com>
> > To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] ViewDock not showing results
> > Message-ID:
> > <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Tried it but you have to save the whole structure, docking included,
> > otherwise you will get only the receptor or the ligand.
> >
> > El lun., 9 de diciembre de 2019 11:32, Elaine Meng <meng at cgl.ucsf.edu>
> > escribi?:
> >
> >> Hi Reshma,
> >> ViewDock is for viewing results that you already calculated using another
> >> program. It does not make these results for you.
> >>
> >> As an example, see tutorials for the DOCK6.9 docking program (not part of
> >> Chimera):
> >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdock.compbio.ucsf.edu%2FDOCK_6%2Ftutorials%2Findex.htm&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741616630&sdata=iEh3oNOUipunkbieGntfIXlx6ALXTYhSERGCDDohJwY%3D&reserved=0>
> >>
> >> If you did get output file(s) from running a separate docking program
> >> (DOCK, Glide, Autodock Vina, etc.) but then ViewDock would not show them,
> >> then we would need an example of that output.
> >>
> >> I changed the subject line to be more descriptive.
> >> Best,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Dec 8, 2019, at 2:19 AM, Reshma Sri Punya <project.mpharma at yahoo.com>
> >> wrote:
> >>>
> >>> Hello good afternoon UCSF chimera is installed in my laptop but not
> >> showing docking results when I use the view dock options it was not showing
> >> any results it's not I tired several times please tell me the solutions to
> >> the problem
> >>
> >>
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> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 11 Dec 2019 14:28:10 +0100
> > From: Harald Lanig <harald.lanig at fau.de>
> > To: <Chimera-users at cgl.ucsf.edu>
> > Subject: [Chimera-users] Conference Announcement: Molecular Modeling
> > Workshop, Feb 17-19, 2020 in Erlangen, Germany
> > Message-ID: <8a26e0fb-caa5-9412-bd2c-2c923b241d93 at fau.de>
> > Content-Type: text/plain; charset="utf-8"; format=flowed
> >
> > Dear list subscribers,
> >
> > we are very delighted to announce this year?s
> >
> > ?34th Molecular Modelling Workshop (MMWS)? (https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmmws2020.mgms-ds.de&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741616630&sdata=jGwfLj69A1MxQi4xr1sZZExUIy7HSfUp0Mi%2FmxTkzXA%3D&reserved=0)
> >
> > that takes place on Monday 17th to Wednesday 19th February 2020
> > at the Friedrich-Alexander-University in Erlangen, Germany.
> >
> > The MMWS has a long history of giving young scientists (especially
> > graduate students) the opportunity to present their work and dive into
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> > ####### Pre-conference Schr?dinger workshop #######
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> > "Electrons in Liquid Ammonia and in Water: From Blue Electrolytes to
> > Bronze Colored Metallic Solutions"
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> > Barbara Kirchner, Bonn
> > "Insights into ionic and molecular liquids and their interfaces from
> > computational chemistry"
> >
> > Charles Laughton, Nottingham
> > "Enhancing conformational sampling with machine learning"
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> > Birgit Strodel, J?lich
> > "Modelling peptide aggregation influenced by in vivo conditions"
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> >
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> > The deadline for all submissions is January 24th, 2020.
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> > ####### General information #######
> > Website https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmmws2020.mgms-ds.de&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741616630&sdata=jGwfLj69A1MxQi4xr1sZZExUIy7HSfUp0Mi%2FmxTkzXA%3D&reserved=0 will provide all necessary
> > information about the meeting.
> >
> > We are looking forward to meeting you in Erlangen!
> > - Christof J?ger, Scientific Committee Workshop Organisation 2020
> > - Harald Lanig, Chairman of the MGMS-DS e.V. (https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mgms-ds.de&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741616630&sdata=A55KwK7SjTJc2Lqp%2BEfd1I2KJWrAVXUkNqWGgxYo49I%3D&reserved=0)
> >
> >
> > --
> > --------------------------------------------------------
> > PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg
> > Zentralinstitut fuer Scientific Computing (ZISC)
> > Forschungsdatenmanagement SFB 814 und SFB 1411
> > Martensstrasse 5a 91058 Erlangen
> > +49 9131-85 20781 harald.lanig at fau.de
> > --------------------------------------------------------
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 11 Dec 2019 17:02:03 +0100
> > From: Damien Larivi?re <damien at fourmentinguilbert.org>
> > To: Chimera-users at cgl.ucsf.edu
> > Subject: [Chimera-users] selection of specific bonds
> > Message-ID:
> > <61dec672-f227-b6ae-6f2d-b91f2662db26 at fourmentinguilbert.org>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> > Dear All,
> >
> > My question is naive but I have difficulties to figure out how to do it
> > with Chimera.
> >
> > I would like to select specifically the group of two atoms (C and O)
> > formed in a carbonyl bond C=O for all, say, GLU residues of a protein.
> >
> > Is there a way, via a command line, to do it?
> >
> > Thanks for your help on this.
> >
> > Damien
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Wed, 11 Dec 2019 09:34:41 -0800
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > To: Damien Larivi?re <damien at fourmentinguilbert.org>
> > Cc: Chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] selection of specific bonds
> > Message-ID: <76257FCF-A7D0-41F2-A71F-DA1114767BF3 at cgl.ucsf.edu>
> > Content-Type: text/plain; charset=utf-8
> >
> > Hi Damien,
> > You?ll like this? simply the command: select carbonyl
> >
> > It selects the atoms as well as the bond between them.
> >
> > You can specify in the command line any of the functional groups that appear in the menu under Select? Chemistry? functional group. It?s mentioned here:
> > <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fatom_spec.html%23builtin&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741626622&sdata=a5f1rNnoCBr9ED408pC8UJ6xRas7fXv8vQfHhhzkk1M%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 Dec 11, 2019, at 8:02 AM, Damien Larivi?re <damien at fourmentinguilbert.org> wrote:
> >>
> >> Dear All,
> >>
> >> My question is naive but I have difficulties to figure out how to do it with Chimera.
> >>
> >> I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein.
> >>
> >> Is there a way, via a command line, to do it?
> >>
> >> Thanks for your help on this.
> >>
> >> Damien
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 11 Dec 2019 10:25:28 -0800
> > From: Eric Pettersen <pett at cgl.ucsf.edu>
> > To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> > Cc: Damien Larivi?re <damien at fourmentinguilbert.org>
> > Subject: Re: [Chimera-users] selection of specific bonds
> > Message-ID: <8C870B19-FA80-4A39-B184-5C5FB33AC2DA at cgl.ucsf.edu>
> > Content-Type: text/plain; charset="utf-8"
> >
> > ? and if you want to find the carbonyls only in GLU residues, you would intersect the specifier with :GLU, i.e.:
> >
> > select carbonyl & :glu
> >
> > ?Eric
> >
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> >
> >
> >
> >> On Dec 11, 2019, at 9:34 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>
> >> Hi Damien,
> >> You?ll like this? simply the command: select carbonyl
> >>
> >> It selects the atoms as well as the bond between them.
> >>
> >> You can specify in the command line any of the functional groups that appear in the menu under Select? Chemistry? functional group. It?s mentioned here:
> >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fatom_spec.html%23builtin&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741626622&sdata=a5f1rNnoCBr9ED408pC8UJ6xRas7fXv8vQfHhhzkk1M%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 Dec 11, 2019, at 8:02 AM, Damien Larivi?re <damien at fourmentinguilbert.org> wrote:
> >>>
> >>> Dear All,
> >>>
> >>> My question is naive but I have difficulties to figure out how to do it with Chimera.
> >>>
> >>> I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein.
> >>>
> >>> Is there a way, via a command line, to do it?
> >>>
> >>> Thanks for your help on this.
> >>>
> >>> Damien
> >>
> >>
> >> _______________________________________________
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> >>
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