[Chimera-users] Volume Eraser

Guo, Wangbiao wangbiao.guo at yale.edu
Thu Dec 12 06:27:09 PST 2019 

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
[cid:1931c4b2-7958-40eb-88a9-6640c394c5b8 at namprd08.prod.outlook.com]

> 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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>>
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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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> ####### Plenary Speakers #######
> We are very happy to announce that five outstanding researchers accepted
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> Petra Imhof, Berlin
> ?Recognition and specificity in protein-DNA interactions - insight from
> molecular simulations?
>
> Pavel Jungwirth, Prague
> "Electrons in Liquid Ammonia and in Water: From Blue Electrolytes to
> Bronze Colored Metallic Solutions"
>
> Barbara Kirchner, Bonn
> "Insights into ionic and molecular liquids and their interfaces from
> computational chemistry"
>
> Charles Laughton, Nottingham
> "Enhancing conformational sampling with machine learning"
>
> Birgit Strodel, J?lich
> "Modelling peptide aggregation influenced by in vivo conditions"
>
>
> ####### Poster and Lecture Awards #######
> As in the past years, there will be two poster awards of EUR 100 each
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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
>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741626622&sdata=dcNVP6clVL%2BndK5xYZxioYV4iZqb5vu4U7lvc%2Bm1lek%3D&reserved=0
>>
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