Location of executable local docking path
Dear Sir, I am performing molecular docking using Autodock vina in Chimera. Could you please guide me how to operate an executable location locally? Which is the file to be loaded in the local path? I will be thankful to you for your kind help *Thanks & Regards* *Dr. Ramesh M* *B. Pharma., M.Pharma., Ph.D. (MedChem)* *Post-Doctoral Fellow (PDF) in Pharmaceutical Sciences* *Researcher ID:* https://orcid.org/0000-0003-0119-206X <https://www.portfoliobox.net/pb4/admin/#/drrameshm> *Website: *https://scholar.google.com/citations?user=VHOE1dgAAAAJ&hl=en Hyderabad, INDIA Email: shreeramesh@gmail.com Mob.: +91-9542200332
The Autodock Vina tool in Chimera has a place to specify the location of the executable, see: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html#location> As to where the executable actually is, it depends on the type of computer you have and where you installed it. However, if you are on Windows, see this previous post, which may help: <https://www.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017696.html> However, this tool in Chimera does not allow very much sampling. For more thorough sampling, you may need to use Autodock Vina directly (not using Chimera). This is mentioned in the gray warning box in the top link above. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2022, at 12:18 AM, Shreeramesh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Sir,
I am performing molecular docking using Autodock vina in Chimera.
Could you please guide me how to operate an executable location locally? Which is the file to be loaded in the local path?
I will be thankful to you for your kind help
Dear Chimera, I have a couple of questions: 1. When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? 2. Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)? Thanks Hernando
Dear Hernando, (1) there is a setting for what size is shown as a plane. In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog. In those options you can turn off (or change the size) for "Show data when opened if smaller than [size] Mvoxels" "Show plane when data larger than [size] Mvoxels" See data display options: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options> Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings" (2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points. See fitmap options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#options> As far as I know, display step size does not affect the calculation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I have a couple of questions: • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
Thanks
Hernando
Hi Hernando, Elaine is right that the displayed step size of the map you are fitting into does not matter -- the fitting will always use the full resolution step 1 data. The displayed subregion of the map you are fitting into does matter -- the fitting will only use the displayed rectangular subregion. It won't do anything if fitting to a single plane (since it needs to be able to interpolate map values in 3 dimensions so it needs at least 2 planes). This allows you to limit the region your atomic model will be fit into by cropping the map display. When fitting one map into another map, both the subregion and the step size for the moving map matter. The fit will be done using values of the moving map at the grid points within the displayed subregion and using the displayed step size. You will see if you change the step size of the moving map it will have a usually very small effect on the fit and reported correlation. I had to look into the code (which I wrote) to be sure of the above rules. If they are not in the documentation we will try to add them since they are important to understand how to setup a fit calculation. Tom
On Feb 1, 2022, at 8:55 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Hernando,
(1) there is a setting for what size is shown as a plane. In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog. In those options you can turn off (or change the size) for
"Show data when opened if smaller than [size] Mvoxels" "Show plane when data larger than [size] Mvoxels"
See data display options: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options>
Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings"
(2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points. See fitmap options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#options>
As far as I know, display step size does not affect the calculation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I have a couple of questions: • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
Thanks
Hernando
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you, Elaine, Another question: does the option to open/display the whole map would also work when using the open command to load the volume and without touching the Volume display dialogue? I am using a script to open and fit several coordinates models with minimal or no GUI use. Also I did notice that if the map is opened/displayed as a single plane then the <fitmap> command does not work as intended. It appears as is the model is fitted to an empty map. A workaround I found was to crop the map before fitting using the command <volume #map region ...>. The cropped map always seems to show all the planes (due to the smaller size?). Best Hernando. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, February 1, 2022 11:55 AM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Volume planes CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. Dear Hernando, (1) there is a setting for what size is shown as a plane. In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog. In those options you can turn off (or change the size) for "Show data when opened if smaller than [size] Mvoxels" "Show plane when data larger than [size] Mvoxels" See data display options: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23disp-options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=7DPQmSVlkp9h%2Fsf7XjLKwLeB896NzGU27QoNjUu3Xf0%3D&reserved=0> Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings" (2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points. See fitmap options: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Ffitmap.html%23options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qc7DeTt5awROTXhRTWPkDJ4JPYxTARpT1TBtnPpunh4%3D&reserved=0> As far as I know, display step size does not affect the calculation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I have a couple of questions: • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
Thanks
Hernando
Hi Hernando, As Tom said, fitting into a plane won't do anything, since it only uses the displayed subregion, which has to be 3-dimensional. I believe that after the settings have been saved as preferences using the Features menu of the Volume Viewer dialog as I described in my first reply (which you would only do once), in later uses of Chimera they will apply to maps regardless of which method was used to open them. There are also corresponding options in the "volume" command, although I'm not sure whether they just apply to the current session or get saved in the preferences. If using the GUI is not possible you could try those: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 1, 2022, at 11:59 AM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you, Elaine,
Another question: does the option to open/display the whole map would also work when using the open command to load the volume and without touching the Volume display dialogue? I am using a script to open and fit several coordinates models with minimal or no GUI use.
Also I did notice that if the map is opened/displayed as a single plane then the <fitmap> command does not work as intended. It appears as is the model is fitted to an empty map. A workaround I found was to crop the map before fitting using the command <volume #map region ...>. The cropped map always seems to show all the planes (due to the smaller size?).
Best
Hernando.
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, February 1, 2022 11:55 AM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Volume planes
CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.
Dear Hernando,
(1) there is a setting for what size is shown as a plane. In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog. In those options you can turn off (or change the size) for
"Show data when opened if smaller than [size] Mvoxels" "Show plane when data larger than [size] Mvoxels"
Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings"
(2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points. See fitmap options: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Ffitmap.html%23options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qc7DeTt5awROTXhRTWPkDJ4JPYxTARpT1TBtnPpunh4%3D&reserved=0>
As far as I know, display step size does not affect the calculation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I have a couple of questions: • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
Thanks
Hernando
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine is right. The open command will use the volume settings saved with the Volume Viewer GUI and that is the only way to save the settings, there is no equivalent command to save the default settings. For a script I'd suggest not relying on special saved default settings. Instead use the volume command to make sure the region and step and level are shown as you want: volume #1 region all step 1 level 3.5 Tom
On Feb 1, 2022, at 12:09 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Hernando, As Tom said, fitting into a plane won't do anything, since it only uses the displayed subregion, which has to be 3-dimensional.
I believe that after the settings have been saved as preferences using the Features menu of the Volume Viewer dialog as I described in my first reply (which you would only do once), in later uses of Chimera they will apply to maps regardless of which method was used to open them.
There are also corresponding options in the "volume" command, although I'm not sure whether they just apply to the current session or get saved in the preferences. If using the GUI is not possible you could try those: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 1, 2022, at 11:59 AM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you, Elaine,
Another question: does the option to open/display the whole map would also work when using the open command to load the volume and without touching the Volume display dialogue? I am using a script to open and fit several coordinates models with minimal or no GUI use.
Also I did notice that if the map is opened/displayed as a single plane then the <fitmap> command does not work as intended. It appears as is the model is fitted to an empty map. A workaround I found was to crop the map before fitting using the command <volume #map region ...>. The cropped map always seems to show all the planes (due to the smaller size?).
Best
Hernando.
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, February 1, 2022 11:55 AM To: Hernando J Sosa <hernando.sosa@einsteinmed.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Volume planes
CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.
Dear Hernando,
(1) there is a setting for what size is shown as a plane. In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog. In those options you can turn off (or change the size) for
"Show data when opened if smaller than [size] Mvoxels" "Show plane when data larger than [size] Mvoxels"
Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings"
(2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points. See fitmap options: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Ffitmap.html%23options&data=04%7C01%7Chernando.sosa%40einsteinmed.edu%7C64a1b9cb12ae413ea3e608d9e5a3ba90%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637793314824180790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qc7DeTt5awROTXhRTWPkDJ4JPYxTARpT1TBtnPpunh4%3D&reserved=0>
As far as I know, display step size does not affect the calculation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I have a couple of questions: • When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size? • Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
Thanks
Hernando
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Hernando J Sosa -
Shreeramesh -
Tom Goddard