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@namprd08.prod.outlook.com]
On Dec 11, 2019, at 1:25 PM, chimera-users-request@cgl.ucsf.edu wrote:
Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit 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%7C637116857741616630&sdata=O7PuyNKum4CZe7cDcz6dta9Mj%2F6AinZNXy%2FwbAF9yI0%3D&reserved=0 or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
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@gmail.com> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] ViewDock not showing results Message-ID: <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@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%7C637116857741616630&sdata=O7PuyNKum4CZe7cDcz6dta9Mj%2F6AinZNXy%2FwbAF9yI0%3D&reserved=0
Dear Seven Guo, Although Volume Eraser does not change your original data set, it first makes a copy and then erases part of the copy. Then you can save the copy (which had parts erased) as a new file. This is mentioned in the documentation shown if you click the Help button on the tool, or at our website here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase.... ...and also the last part of this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-December/016348.html> 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 12, 2019, at 6:27 AM, Guo, Wangbiao <wangbiao.guo@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>
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@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@cgl.ucsf.edu wrote:
Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit 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%7C637116857741616630&sdata=O7PuyNKum4CZe7cDcz6dta9Mj%2F6AinZNXy%2FwbAF9yI0%3D&reserved=0 or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
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@gmail.com> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] ViewDock not showing results Message-ID: <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@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%7C637116857741616630&sdata=O7PuyNKum4CZe7cDcz6dta9Mj%2F6AinZNXy%2FwbAF9yI0%3D&reserved=0
participants (3)
-
Elaine Meng -
Guo, Wangbiao -
Tom Goddard