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<div class="PlainText">Dear all:<br>
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.<br>
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<br>
Seven Guo<br>
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> On Dec 11, 2019, at 1:25 PM, chimera-users-request@cgl.ucsf.edu wrote:<br>
> <br>
> Send Chimera-users mailing list submissions to<br>
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> <br>
> Today's Topics:<br>
> <br>
> 1. Re: ViewDock not showing results (Don Gabo)<br>
> 2. Conference Announcement: Molecular Modeling Workshop, Feb<br>
> 17-19, 2020 in Erlangen, Germany (Harald Lanig)<br>
> 3. selection of specific bonds (Damien Larivi?re)<br>
> 4. Re: selection of specific bonds (Elaine Meng)<br>
> 5. Re: selection of specific bonds (Eric Pettersen)<br>
> <br>
> <br>
> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Mon, 9 Dec 2019 13:10:30 -0600<br>
> From: Don Gabo <gabrielsrbio@gmail.com><br>
> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
> Subject: Re: [Chimera-users] ViewDock not showing results<br>
> Message-ID:<br>
> <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw@mail.gmail.com><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> Tried it but you have to save the whole structure, docking included,<br>
> otherwise you will get only the receptor or the ligand.<br>
> <br>
> El lun., 9 de diciembre de 2019 11:32, Elaine Meng <meng@cgl.ucsf.edu><br>
> escribi?:<br>
> <br>
>> Hi Reshma,<br>
>> ViewDock is for viewing results that you already calculated using another<br>
>> program. It does not make these results for you.<br>
>> <br>
>> As an example, see tutorials for the DOCK6.9 docking program (not part of<br>
>> Chimera):<br>
>> <<a href="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">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</a>><br>
>> <br>
>> If you did get output file(s) from running a separate docking program<br>
>> (DOCK, Glide, Autodock Vina, etc.) but then ViewDock would not show them,<br>
>> then we would need an example of that output.<br>
>> <br>
>> I changed the subject line to be more descriptive.<br>
>> Best,<br>
>> Elaine<br>
>> -----<br>
>> Elaine C. Meng, Ph.D.<br>
>> UCSF Chimera(X) team<br>
>> Department of Pharmaceutical Chemistry<br>
>> University of California, San Francisco<br>
>> <br>
>>> On Dec 8, 2019, at 2:19 AM, Reshma Sri Punya <project.mpharma@yahoo.com><br>
>> wrote:<br>
>>> <br>
>>> Hello good afternoon UCSF chimera is installed in my laptop but not<br>
>> showing docking results when I use the view dock options it was not showing<br>
>> any results it's not I tired several times please tell me the solutions to<br>
>> the problem<br>
>> <br>
>> <br>
>> _______________________________________________<br>
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> ------------------------------<br>
> <br>
> Message: 2<br>
> Date: Wed, 11 Dec 2019 14:28:10 +0100<br>
> From: Harald Lanig <harald.lanig@fau.de><br>
> To: <Chimera-users@cgl.ucsf.edu><br>
> Subject: [Chimera-users] Conference Announcement: Molecular Modeling<br>
> Workshop, Feb 17-19, 2020 in Erlangen, Germany<br>
> Message-ID: <8a26e0fb-caa5-9412-bd2c-2c923b241d93@fau.de><br>
> Content-Type: text/plain; charset="utf-8"; format=flowed<br>
> <br>
> Dear list subscribers,<br>
> <br>
> we are very delighted to announce this year?s<br>
> <br>
> ?34th Molecular Modelling Workshop (MMWS)? (<a href="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">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</a>)<br>
> <br>
> that takes place on Monday 17th to Wednesday 19th February 2020<br>
> at the Friedrich-Alexander-University in Erlangen, Germany.<br>
> <br>
> The MMWS has a long history of giving young scientists (especially<br>
> graduate students) the opportunity to present their work and dive into<br>
> discussions with each other and the "older experts" of the field to gain<br>
> valuable feedback from academic as well as industrial colleagues. Oral<br>
> and poster contributions are welcome from all areas of molecular<br>
> modelling ? from the life sciences, computational biology and chemistry,<br>
> cheminformatics, to materials sciences.<br>
> <br>
> Starting with the scientific program on Monday after lunch should allow<br>
> to avoid travelling on weekend keeping the expenses at a minimum. Once<br>
> again the location changed - back to the roots we are now back again<br>
> in the Organic Chemistry building at Henkestrasse 42.<br>
> A hearty workshop dinner and a traditional joint evening in Erlangen?s<br>
> Steinbach-Br?u brewery complement the scientific program. The workshop<br>
> is organised by the German Section of the Molecular Graphics and<br>
> Modelling Society (MGMS-DS e.V.).<br>
> <br>
> ####### Pre-conference Schr?dinger workshop #######<br>
> For the third time at our Molecular Modeling Workshop, Schr?dinger is<br>
> offering a pre-conference workshop entiteled "Structure-based Drug<br>
> Design using the Schr?dinger Suite". If you are interested in<br>
> participating at the software session, please checkmark the<br>
> corresponding field upon filling the registration form. Please note that<br>
> this event is taking place at the CCC in Naegelsbachstrasse 25.<br>
> <br>
> ####### Plenary Speakers #######<br>
> We are very happy to announce that five outstanding researchers accepted<br>
> our invitation to present a plenary lecture at the Modeling workshop:<br>
> <br>
> Petra Imhof, Berlin<br>
> ?Recognition and specificity in protein-DNA interactions - insight from<br>
> molecular simulations?<br>
> <br>
> Pavel Jungwirth, Prague<br>
> "Electrons in Liquid Ammonia and in Water: From Blue Electrolytes to<br>
> Bronze Colored Metallic Solutions"<br>
> <br>
> Barbara Kirchner, Bonn<br>
> "Insights into ionic and molecular liquids and their interfaces from<br>
> computational chemistry"<br>
> <br>
> Charles Laughton, Nottingham<br>
> "Enhancing conformational sampling with machine learning"<br>
> <br>
> Birgit Strodel, J?lich<br>
> "Modelling peptide aggregation influenced by in vivo conditions"<br>
> <br>
> <br>
> ####### Poster and Lecture Awards #######<br>
> As in the past years, there will be two poster awards of EUR 100 each<br>
> and three lecture awards for the best contributed oral presentations:<br>
> <br>
> 1st winner: Travel bursary to attend the Young Modeller's Forum in<br>
> London, UK, plus a speaker slot option at YMF (travel expenses are<br>
> reimbursed up to EUR 500)<br>
> 2nd winner: EUR 200 travel expenses reimbursement<br>
> 3rd winner: EUR 100 travel expenses reimbursement<br>
> <br>
> Only undergraduate and graduate research students qualify for the poster<br>
> and lecture awards.<br>
> <br>
> ####### Registration and poster/talk submission #######<br>
> Submit talks and/or poster titles via the registration form accessible<br>
> on the workshop website <a href="https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmmws2020.mgms-ds.de%2Findex.php%3Fm%3Dregister&data=02%7C01%7Cwangbiao.guo%40yale.edu%7C1b2dc4dee0e24265d3f308d77e680ecc%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C637116857741616630&sdata=cWJX2fo1dmU6PRVskqFbozWiTNzFnag7AszqgN4SG5c%3D&reserved=0">
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> The deadline for all submissions is January 24th, 2020.<br>
> <br>
> ####### General information #######<br>
> Website <a href="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">
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will provide all necessary<br>
> information about the meeting.<br>
> <br>
> We are looking forward to meeting you in Erlangen!<br>
> - Christof J?ger, Scientific Committee Workshop Organisation 2020<br>
> - Harald Lanig, Chairman of the MGMS-DS e.V. (<a href="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">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</a>)<br>
> <br>
> <br>
> -- <br>
> --------------------------------------------------------<br>
> PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg<br>
> Zentralinstitut fuer Scientific Computing (ZISC)<br>
> Forschungsdatenmanagement SFB 814 und SFB 1411<br>
> Martensstrasse 5a 91058 Erlangen<br>
> +49 9131-85 20781 harald.lanig@fau.de<br>
> --------------------------------------------------------<br>
> <br>
> <br>
> <br>
> ------------------------------<br>
> <br>
> Message: 3<br>
> Date: Wed, 11 Dec 2019 17:02:03 +0100<br>
> From: Damien Larivi?re <damien@fourmentinguilbert.org><br>
> To: Chimera-users@cgl.ucsf.edu<br>
> Subject: [Chimera-users] selection of specific bonds<br>
> Message-ID:<br>
> <61dec672-f227-b6ae-6f2d-b91f2662db26@fourmentinguilbert.org><br>
> Content-Type: text/plain; charset=utf-8; format=flowed<br>
> <br>
> Dear All,<br>
> <br>
> My question is naive but I have difficulties to figure out how to do it <br>
> with Chimera.<br>
> <br>
> I would like to select specifically the group of two atoms (C and O) <br>
> formed in a carbonyl bond C=O for all, say, GLU residues of a protein.<br>
> <br>
> Is there a way, via a command line, to do it?<br>
> <br>
> Thanks for your help on this.<br>
> <br>
> Damien<br>
> <br>
> <br>
> <br>
> ------------------------------<br>
> <br>
> Message: 4<br>
> Date: Wed, 11 Dec 2019 09:34:41 -0800<br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> To: Damien Larivi?re <damien@fourmentinguilbert.org><br>
> Cc: Chimera-users@cgl.ucsf.edu<br>
> Subject: Re: [Chimera-users] selection of specific bonds<br>
> Message-ID: <76257FCF-A7D0-41F2-A71F-DA1114767BF3@cgl.ucsf.edu><br>
> Content-Type: text/plain; charset=utf-8<br>
> <br>
> Hi Damien,<br>
> You?ll like this? simply the command: select carbonyl<br>
> <br>
> It selects the atoms as well as the bond between them.<br>
> <br>
> 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:<br>
> <<a href="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">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</a>><br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
>> On Dec 11, 2019, at 8:02 AM, Damien Larivi?re <damien@fourmentinguilbert.org> wrote:<br>
>> <br>
>> Dear All,<br>
>> <br>
>> My question is naive but I have difficulties to figure out how to do it with Chimera.<br>
>> <br>
>> 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.<br>
>> <br>
>> Is there a way, via a command line, to do it?<br>
>> <br>
>> Thanks for your help on this.<br>
>> <br>
>> Damien<br>
> <br>
> <br>
> <br>
> <br>
> ------------------------------<br>
> <br>
> Message: 5<br>
> Date: Wed, 11 Dec 2019 10:25:28 -0800<br>
> From: Eric Pettersen <pett@cgl.ucsf.edu><br>
> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu><br>
> Cc: Damien Larivi?re <damien@fourmentinguilbert.org><br>
> Subject: Re: [Chimera-users] selection of specific bonds<br>
> Message-ID: <8C870B19-FA80-4A39-B184-5C5FB33AC2DA@cgl.ucsf.edu><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> ? and if you want to find the carbonyls only in GLU residues, you would intersect the specifier with :GLU, i.e.:<br>
> <br>
> select carbonyl & :glu<br>
> <br>
> ?Eric<br>
> <br>
> Eric Pettersen<br>
> UCSF Computer Graphics Lab<br>
> <br>
> <br>
> <br>
>> On Dec 11, 2019, at 9:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br>
>> <br>
>> Hi Damien,<br>
>> You?ll like this? simply the command: select carbonyl<br>
>> <br>
>> It selects the atoms as well as the bond between them.<br>
>> <br>
>> 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:<br>
>> <<a href="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">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</a>><br>
>> <br>
>> I hope this helps,<br>
>> Elaine<br>
>> -----<br>
>> Elaine C. Meng, Ph.D.<br>
>> UCSF Chimera(X) team<br>
>> Department of Pharmaceutical Chemistry<br>
>> University of California, San Francisco<br>
>> <br>
>>> On Dec 11, 2019, at 8:02 AM, Damien Larivi?re <damien@fourmentinguilbert.org> wrote:<br>
>>> <br>
>>> Dear All,<br>
>>> <br>
>>> My question is naive but I have difficulties to figure out how to do it with Chimera.<br>
>>> <br>
>>> 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.<br>
>>> <br>
>>> Is there a way, via a command line, to do it?<br>
>>> <br>
>>> Thanks for your help on this.<br>
>>> <br>
>>> Damien<br>
>> <br>
>> <br>
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