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From: Jose M. de la R. T. <del...@gm...> - 2019-11-01 10:30:33
|
Hi Daniel, Scipion itself does not use CUDA itself, that's why CUDA=False... but you can still use the plugins with other cuda-programs (e.g Relion, cryolo). I know this is a bit confusing, sorry for that. ;) Just make sure that you set the CUDA_LIB and other related variables properly. You can define those different for each program (e.g en case the binaries depends on different cuda versions) Best, Jose Miguel On Fri, Nov 1, 2019 at 11:23 AM Daniel Larsson <dan...@ic...> wrote: > > > On 2019-11-01, at 11:14, Daniel Larsson <dan...@ic...> wrote: > > > > On 2019-10-31, at 11:32, Pablo Conesa <pc...@CN...> wrote: > > Hi Daniel, > > About XMIPP: > > You probably have the plugin (python code that wrapps xmipp) but not the > actual xmipp. > > Try scipion installb > > I'm getting: > > xmippBin_Centos 3.19.04 [ ] > xmippBin_Debian 3.19.04 [ ] > xmippSrc 3.19.04 [X] > > First ones are compiled xmipp for Centos and Debian. > > 3rd are sources and will require compiling xmipp, but probably safer in > terms of dependencies. > > > Running "scipion installb" revealed that I indeed do not have xmipp > installed. I did not realize that you could drill down for Xmipp in the > Plugin Manager GUI. When I tried installing xmippSrc, it turns out that I > have a too old g++ compiler (needs 4.8 or later). I guess that is why I did > not get xmipp in the first place. Now I figured out how to use g++ version > 7.3.1, but run into problems with missing opencv headers. I don't think I > will need such features and wondering how I should customize my > installation to run with "--no-opencv". Where should I edit? > > > Ok, found the OPENCV = True/False flag in config/scipion.conf thanks to > some googling: > https://sourceforge.net/p/scipion/mailman/message/36738786/ > > Also while digging around in the scipion.conf file, I realized that I have > CUDA = False. I guess I should remove all plugins and recompile them with > the CUDA = True if I want Relion with CUDA, right? > > > > > About CONDA_ACTIVATION_CMD: > > Some plugins, (in your case sphire) require to have conda installed. Conda > installation ask you to "add itself" to the shell so you have conda in the > PATH. > > When doing so, python calls, in some cases are messed up due to having > conda and its python exposed in the terminal. > > We recommend not to have conda initialized in the terminal and tell > scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD" > > > In my case I got this in the <Scipion-home>/config/scipion.conf under > BUILD section: > > CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash > hook)" > > NOTE: Conda usually tells you that command. see > https://github.com/scipion-em/scipion-em-sphire#cryolo-integration > > Ok. I don't think there is Conda available. I'll uninstall Sphire/cryolo > for the time being. > > > About Locascale: Locscale plugin has a dependency to Eman plugin, try to > install eman plugin: > > scipion installp -p scipion-em-eman2 > > Ok. Fixed that! > > > > > On 31/10/19 10:55, Daniel Larsson wrote: > > So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions? > > Regards, > Daniel > > > > > > > scipion installp --help --checkUpdates > > Scipion v2.0 (2019-04-23) Diocletian > > > python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates > > >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp in Scipion manager window) > > > error when importing from eman2: No module named PyQt4 > Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34 > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > Warning: couldn't find Plugin for scipion-em-locscale > Dirname: locscale > WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH > usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]] > > optional arguments: > -h, --help show help > --noBin Optional flag to install plugins only as a python module, > without installing the plugin binaries. This will affect > all plugins specified in the command. > --checkUpdates Optional flag to check which plugins have new releases. > -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...] > - pluginName: the name of the plugin to install from the list > of available plugins shown below. > - pluginVersion: (optional) pip version to install. If not specified, > will install the latest compatible with current Scipion. > --devel Optional flag to indicate that we will pass install sources instead > of pip names. Sources might be local paths or git urls. With local > paths, will do pip install -e (editable mode). It is expected to find > the plugin name in the basename of the path or in the repo name. > (i.e. it needs to match the one specified in setup.py). E.g: > scipion installp -p path/to/pluginName --devel > scipion installp -p https://github.com/someOrg/pluginName.git --devel > -j j Number of CPUs to use for compilation > > Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2 > > Available plugins: ([ ] not installed, [X] seems already installed) > > scipion-em-appion 1.0.2 [X] > scipion-em-atomstructutils 1.0.7 [X] > scipion-em-atsas 1.0.6 [X] > scipion-em-bamfordlab [ ] > scipion-em-bsoft 1.0.3 [X] > scipion-em-ccp4 1.0.12 [X] > scipion-em-chimera 1.0.2 [X] > scipion-em-cryoef 1.0.5 [X] > scipion-em-cryomethods [ ] > scipion-em-cryosparc2 1.0.7 [X] > scipion-em-eman2 [ ] > scipion-em-empiar 1.0.3 [X] > scipion-em-emxlib [ ] > scipion-em-esrf [ ] > scipion-em-gautomatch 1.0.7 [X] > scipion-em-gctf 1.0.7 [X] > scipion-em-grigoriefflab 1.0.6 [X] > scipion-em-imagic [ ] > scipion-em-ispyb [ ] > scipion-em-localrec 2.0 [X] > scipion-em-locscale 1.0.5 [X] > scipion-em-motioncorr 1.0.4 [X] > scipion-em-nysbc [ ] > scipion-em-phenix [ ] > scipion-em-powerfit [ ] > scipion-em-relion 1.0.7 [X] > scipion-em-resmap 1.0.5 [X] > scipion-em-simple [ ] > scipion-em-sphire 1.2.9 [X] > scipion-em-spider [ ] > scipion-em-topaz [ ] > scipion-em-xmipp 19.4.3 [X] > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Daniel L. <dan...@ic...> - 2019-11-01 10:22:52
|
On 2019-11-01, at 11:14, Daniel Larsson <dan...@ic...<mailto:dan...@ic...>> wrote:
On 2019-10-31, at 11:32, Pablo Conesa <pc...@CN...<mailto:pc...@CN...>> wrote:
Hi Daniel,
About XMIPP:
You probably have the plugin (python code that wrapps xmipp) but not the actual xmipp.
Try scipion installb
I'm getting:
xmippBin_Centos 3.19.04 [ ]
xmippBin_Debian 3.19.04 [ ]
xmippSrc 3.19.04 [X]
First ones are compiled xmipp for Centos and Debian.
3rd are sources and will require compiling xmipp, but probably safer in terms of dependencies.
Running "scipion installb" revealed that I indeed do not have xmipp installed. I did not realize that you could drill down for Xmipp in the Plugin Manager GUI. When I tried installing xmippSrc, it turns out that I have a too old g++ compiler (needs 4.8 or later). I guess that is why I did not get xmipp in the first place. Now I figured out how to use g++ version 7.3.1, but run into problems with missing opencv headers. I don't think I will need such features and wondering how I should customize my installation to run with "--no-opencv". Where should I edit?
Ok, found the OPENCV = True/False flag in config/scipion.conf thanks to some googling:
https://sourceforge.net/p/scipion/mailman/message/36738786/
Also while digging around in the scipion.conf file, I realized that I have CUDA = False. I guess I should remove all plugins and recompile them with the CUDA = True if I want Relion with CUDA, right?
About CONDA_ACTIVATION_CMD:
Some plugins, (in your case sphire) require to have conda installed. Conda installation ask you to "add itself" to the shell so you have conda in the PATH.
When doing so, python calls, in some cases are messed up due to having conda and its python exposed in the terminal.
We recommend not to have conda initialized in the terminal and tell scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD"
In my case I got this in the <Scipion-home>/config/scipion.conf under BUILD section:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
NOTE: Conda usually tells you that command. see https://github.com/scipion-em/scipion-em-sphire#cryolo-integration
Ok. I don't think there is Conda available. I'll uninstall Sphire/cryolo for the time being.
About Locascale: Locscale plugin has a dependency to Eman plugin, try to install eman plugin:
scipion installp -p scipion-em-eman2
Ok. Fixed that!
On 31/10/19 10:55, Daniel Larsson wrote:
So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions?
Regards,
Daniel
scipion installp --help --checkUpdates
Scipion v2.0 (2019-04-23) Diocletian
python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates
>>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
> error when importing from eman2: No module named PyQt4
Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Warning: couldn't find Plugin for scipion-em-locscale
Dirname: locscale
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em-appion 1.0.2 [X]
scipion-em-atomstructutils 1.0.7 [X]
scipion-em-atsas 1.0.6 [X]
scipion-em-bamfordlab [ ]
scipion-em-bsoft 1.0.3 [X]
scipion-em-ccp4 1.0.12 [X]
scipion-em-chimera 1.0.2 [X]
scipion-em-cryoef 1.0.5 [X]
scipion-em-cryomethods [ ]
scipion-em-cryosparc2 1.0.7 [X]
scipion-em-eman2 [ ]
scipion-em-empiar 1.0.3 [X]
scipion-em-emxlib [ ]
scipion-em-esrf [ ]
scipion-em-gautomatch 1.0.7 [X]
scipion-em-gctf 1.0.7 [X]
scipion-em-grigoriefflab 1.0.6 [X]
scipion-em-imagic [ ]
scipion-em-ispyb [ ]
scipion-em-localrec 2.0 [X]
scipion-em-locscale 1.0.5 [X]
scipion-em-motioncorr 1.0.4 [X]
scipion-em-nysbc [ ]
scipion-em-phenix [ ]
scipion-em-powerfit [ ]
scipion-em-relion 1.0.7 [X]
scipion-em-resmap 1.0.5 [X]
scipion-em-simple [ ]
scipion-em-sphire 1.2.9 [X]
scipion-em-spider [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 19.4.3 [X]
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Daniel L. <dan...@ic...> - 2019-11-01 10:14:19
|
On 2019-10-31, at 11:32, Pablo Conesa <pc...@CN...<mailto:pc...@CN...>> wrote:
Hi Daniel,
About XMIPP:
You probably have the plugin (python code that wrapps xmipp) but not the actual xmipp.
Try scipion installb
I'm getting:
xmippBin_Centos 3.19.04 [ ]
xmippBin_Debian 3.19.04 [ ]
xmippSrc 3.19.04 [X]
First ones are compiled xmipp for Centos and Debian.
3rd are sources and will require compiling xmipp, but probably safer in terms of dependencies.
Running "scipion installb" revealed that I indeed do not have xmipp installed. I did not realize that you could drill down for Xmipp in the Plugin Manager GUI. When I tried installing xmippSrc, it turns out that I have a too old g++ compiler (needs 4.8 or later). I guess that is why I did not get xmipp in the first place. Now I figured out how to use g++ version 7.3.1, but run into problems with missing opencv headers. I don't think I will need such features and wondering how I should customize my installation to run with "--no-opencv". Where should I edit?
About CONDA_ACTIVATION_CMD:
Some plugins, (in your case sphire) require to have conda installed. Conda installation ask you to "add itself" to the shell so you have conda in the PATH.
When doing so, python calls, in some cases are messed up due to having conda and its python exposed in the terminal.
We recommend not to have conda initialized in the terminal and tell scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD"
In my case I got this in the <Scipion-home>/config/scipion.conf under BUILD section:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
NOTE: Conda usually tells you that command. see https://github.com/scipion-em/scipion-em-sphire#cryolo-integration
Ok. I don't think there is Conda available. I'll uninstall Sphire/cryolo for the time being.
About Locascale: Locscale plugin has a dependency to Eman plugin, try to install eman plugin:
scipion installp -p scipion-em-eman2
Ok. Fixed that!
On 31/10/19 10:55, Daniel Larsson wrote:
So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions?
Regards,
Daniel
scipion installp --help --checkUpdates
Scipion v2.0 (2019-04-23) Diocletian
python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates
>>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
> error when importing from eman2: No module named PyQt4
Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Warning: couldn't find Plugin for scipion-em-locscale
Dirname: locscale
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em-appion 1.0.2 [X]
scipion-em-atomstructutils 1.0.7 [X]
scipion-em-atsas 1.0.6 [X]
scipion-em-bamfordlab [ ]
scipion-em-bsoft 1.0.3 [X]
scipion-em-ccp4 1.0.12 [X]
scipion-em-chimera 1.0.2 [X]
scipion-em-cryoef 1.0.5 [X]
scipion-em-cryomethods [ ]
scipion-em-cryosparc2 1.0.7 [X]
scipion-em-eman2 [ ]
scipion-em-empiar 1.0.3 [X]
scipion-em-emxlib [ ]
scipion-em-esrf [ ]
scipion-em-gautomatch 1.0.7 [X]
scipion-em-gctf 1.0.7 [X]
scipion-em-grigoriefflab 1.0.6 [X]
scipion-em-imagic [ ]
scipion-em-ispyb [ ]
scipion-em-localrec 2.0 [X]
scipion-em-locscale 1.0.5 [X]
scipion-em-motioncorr 1.0.4 [X]
scipion-em-nysbc [ ]
scipion-em-phenix [ ]
scipion-em-powerfit [ ]
scipion-em-relion 1.0.7 [X]
scipion-em-resmap 1.0.5 [X]
scipion-em-simple [ ]
scipion-em-sphire 1.2.9 [X]
scipion-em-spider [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 19.4.3 [X]
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--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team
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From: Pablo C. <pc...@cn...> - 2019-10-31 10:32:40
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Hi Daniel, About XMIPP: You probably have the plugin (python code that wrapps xmipp) but not the actual xmipp. Try scipion installb I'm getting: xmippBin_Centos 3.19.04 [ ] xmippBin_Debian 3.19.04 [ ] xmippSrc 3.19.04 [X] First ones are compiled xmipp for Centos and Debian. 3rd are sources and will require compiling xmipp, but probably safer in terms of dependencies. About CONDA_ACTIVATION_CMD: Some plugins, (in your case sphire) require to have conda installed. Conda installation ask you to "add itself" to the shell so you have conda in the PATH. When doing so, python calls, in some cases are messed up due to having conda and its python exposed in the terminal. We recommend not to have conda initialized in the terminal and tell scipion how to activate conda using the variable "CONDA_ACTIVATION_CMD" In my case I got this in the <Scipion-home>/config/scipion.conf under BUILD section: CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)" NOTE: Conda usually tells you that command. see https://github.com/scipion-em/scipion-em-sphire#cryolo-integration About Locascale: Locscale plugin has a dependency to Eman plugin, try to install eman plugin: scipion installp -p scipion-em-eman2 On 31/10/19 10:55, Daniel Larsson wrote: > So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions? > > Regards, > Daniel > > > > > >> scipion installp --help --checkUpdates > Scipion v2.0 (2019-04-23) Diocletian > >>>>>> python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates > >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp in Scipion manager window) > > > error when importing from eman2: No module named PyQt4 > Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34 > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > Warning: couldn't find Plugin for scipion-em-locscale > Dirname: locscale > WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH > usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]] > > optional arguments: > -h, --help show help > --noBin Optional flag to install plugins only as a python module, > without installing the plugin binaries. This will affect > all plugins specified in the command. > --checkUpdates Optional flag to check which plugins have new releases. > -p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...] > - pluginName: the name of the plugin to install from the list > of available plugins shown below. > - pluginVersion: (optional) pip version to install. If not specified, > will install the latest compatible with current Scipion. > --devel Optional flag to indicate that we will pass install sources instead > of pip names. Sources might be local paths or git urls. With local > paths, will do pip install -e (editable mode). It is expected to find > the plugin name in the basename of the path or in the repo name. > (i.e. it needs to match the one specified in setup.py). E.g: > scipion installp -p path/to/pluginName --devel > scipion installp -p https://github.com/someOrg/pluginName.git --devel > -j j Number of CPUs to use for compilation > > Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2 > > Available plugins: ([ ] not installed, [X] seems already installed) > > scipion-em-appion 1.0.2 [X] > scipion-em-atomstructutils 1.0.7 [X] > scipion-em-atsas 1.0.6 [X] > scipion-em-bamfordlab [ ] > scipion-em-bsoft 1.0.3 [X] > scipion-em-ccp4 1.0.12 [X] > scipion-em-chimera 1.0.2 [X] > scipion-em-cryoef 1.0.5 [X] > scipion-em-cryomethods [ ] > scipion-em-cryosparc2 1.0.7 [X] > scipion-em-eman2 [ ] > scipion-em-empiar 1.0.3 [X] > scipion-em-emxlib [ ] > scipion-em-esrf [ ] > scipion-em-gautomatch 1.0.7 [X] > scipion-em-gctf 1.0.7 [X] > scipion-em-grigoriefflab 1.0.6 [X] > scipion-em-imagic [ ] > scipion-em-ispyb [ ] > scipion-em-localrec 2.0 [X] > scipion-em-locscale 1.0.5 [X] > scipion-em-motioncorr 1.0.4 [X] > scipion-em-nysbc [ ] > scipion-em-phenix [ ] > scipion-em-powerfit [ ] > scipion-em-relion 1.0.7 [X] > scipion-em-resmap 1.0.5 [X] > scipion-em-simple [ ] > scipion-em-sphire 1.2.9 [X] > scipion-em-spider [ ] > scipion-em-topaz [ ] > scipion-em-xmipp 19.4.3 [X] > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Daniel L. <dan...@ic...> - 2019-10-31 09:55:51
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So I just installed Scipion 2.0 on a CentOS cluster and installed some plugins using the Plugin Manger and get some warnings. First, I installed Xmipp, but I stil get a warning about missing Xmipp binaries when I start Scipion. I ran the scipion installp --help --checkUpdates command (see below for the output). There are also warnings about locscale and eman2/PyQt4. And what is the CONDA warning about? Any suggestions?
Regards,
Daniel
> scipion installp --help --checkUpdates
Scipion v2.0 (2019-04-23) Diocletian
>>>>> python /home/larsson/software/scipion_v2.0/pyworkflow/install/install-plugin.py /home/larsson/software/scipion_v2.0/scipion installp --help --checkUpdates
>>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
> error when importing from eman2: No module named PyQt4
Called by /home/larsson/software/scipion_v2.0/software/lib/python2.7/site-packages/locscale/constants.py, line 34
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
Warning: couldn't find Plugin for scipion-em-locscale
Dirname: locscale
WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH
usage: /home/larsson/software/scipion_v2.0/scipion installp [-h] [--noBin] [-p pluginName [pipVersion ...]]
optional arguments:
-h, --help show help
--noBin Optional flag to install plugins only as a python module,
without installing the plugin binaries. This will affect
all plugins specified in the command.
--checkUpdates Optional flag to check which plugins have new releases.
-p pluginName [pluginVersion ...], --plugin pluginName [pluginVersion ...]
- pluginName: the name of the plugin to install from the list
of available plugins shown below.
- pluginVersion: (optional) pip version to install. If not specified,
will install the latest compatible with current Scipion.
--devel Optional flag to indicate that we will pass install sources instead
of pip names. Sources might be local paths or git urls. With local
paths, will do pip install -e (editable mode). It is expected to find
the plugin name in the basename of the path or in the repo name.
(i.e. it needs to match the one specified in setup.py). E.g:
scipion installp -p path/to/pluginName --devel
scipion installp -p https://github.com/someOrg/pluginName.git --devel
-j j Number of CPUs to use for compilation
Example: /home/larsson/software/scipion_v2.0/scipion installp -p scipion-em-grigoriefflab 1.0.1 -p scipion-em-relion -p scipion-em-eman2
Available plugins: ([ ] not installed, [X] seems already installed)
scipion-em-appion 1.0.2 [X]
scipion-em-atomstructutils 1.0.7 [X]
scipion-em-atsas 1.0.6 [X]
scipion-em-bamfordlab [ ]
scipion-em-bsoft 1.0.3 [X]
scipion-em-ccp4 1.0.12 [X]
scipion-em-chimera 1.0.2 [X]
scipion-em-cryoef 1.0.5 [X]
scipion-em-cryomethods [ ]
scipion-em-cryosparc2 1.0.7 [X]
scipion-em-eman2 [ ]
scipion-em-empiar 1.0.3 [X]
scipion-em-emxlib [ ]
scipion-em-esrf [ ]
scipion-em-gautomatch 1.0.7 [X]
scipion-em-gctf 1.0.7 [X]
scipion-em-grigoriefflab 1.0.6 [X]
scipion-em-imagic [ ]
scipion-em-ispyb [ ]
scipion-em-localrec 2.0 [X]
scipion-em-locscale 1.0.5 [X]
scipion-em-motioncorr 1.0.4 [X]
scipion-em-nysbc [ ]
scipion-em-phenix [ ]
scipion-em-powerfit [ ]
scipion-em-relion 1.0.7 [X]
scipion-em-resmap 1.0.5 [X]
scipion-em-simple [ ]
scipion-em-sphire 1.2.9 [X]
scipion-em-spider [ ]
scipion-em-topaz [ ]
scipion-em-xmipp 19.4.3 [X]
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
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From: Pablo C. <pc...@cn...> - 2019-10-31 08:18:59
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yep, tmp can be deleted and git stuff too. On 31/10/19 9:14, Daniel Larsson wrote: > HI Jose and Pablo, > > Thanks a lot for the quick feedback! > > I'll go ahead and copy everything over. I guess I can exclude the > .git* stuff and perhaps also software/tmp? > > Regards, > Daniel > > >> On 2019-10-31, at 09:08, Pablo Conesa <pc...@cn... >> <mailto:pc...@cn...>> wrote: >> >> Hi Daniel! >> >> You can move the whole folder. It should work. There was an issue >> before with eman installation, that had to hardcode the path and when >> moving the scipion folder eman was broken. >> >> It should be ok to install eman after moving scipion. >> >> On 31/10/19 8:39, Daniel Larsson wrote: >>> I've built scipion 2.0 from the git source and was now wondering how to finish the installation. I would like to have the binaries in a custom location and not the git source directory. Is there a configure variable that I should have set or can I just move some directories (if so, which?) without breaking the build? >>> >>> Regards, >>> Daniel >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här:http://www.uu.se/om-uu/dataskydd-personuppgifter/ >>> >>> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here:http://www.uu.se/en/about-uu/data-protection-policy >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Daniel L. <dan...@ic...> - 2019-10-31 08:15:01
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HI Jose and Pablo, Thanks a lot for the quick feedback! I'll go ahead and copy everything over. I guess I can exclude the .git* stuff and perhaps also software/tmp? Regards, Daniel On 2019-10-31, at 09:08, Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote: Hi Daniel! You can move the whole folder. It should work. There was an issue before with eman installation, that had to hardcode the path and when moving the scipion folder eman was broken. It should be ok to install eman after moving scipion. On 31/10/19 8:39, Daniel Larsson wrote: I've built scipion 2.0 from the git source and was now wondering how to finish the installation. I would like to have the binaries in a custom location and not the git source directory. Is there a configure variable that I should have set or can I just move some directories (if so, which?) without breaking the build? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es/> team _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2019-10-31 08:08:27
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Hi Daniel! You can move the whole folder. It should work. There was an issue before with eman installation, that had to hardcode the path and when moving the scipion folder eman was broken. It should be ok to install eman after moving scipion. On 31/10/19 8:39, Daniel Larsson wrote: > I've built scipion 2.0 from the git source and was now wondering how to finish the installation. I would like to have the binaries in a custom location and not the git source directory. Is there a configure variable that I should have set or can I just move some directories (if so, which?) without breaking the build? > > Regards, > Daniel > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Jose M. de la R. T. <del...@gm...> - 2019-10-31 08:05:11
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Hi Daniel, Once built, you can move the Scipion directory to any other location. Please let me know if you have any questions. Kind regards, Jose Miguel On Thu, Oct 31, 2019 at 8:57 AM Daniel Larsson <dan...@ic...> wrote: > I've built scipion 2.0 from the git source and was now wondering how to > finish the installation. I would like to have the binaries in a custom > location and not the git source directory. Is there a configure variable > that I should have set or can I just move some directories (if so, which?) > without breaking the build? > > Regards, > Daniel > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Daniel L. <dan...@ic...> - 2019-10-31 07:56:59
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I've built scipion 2.0 from the git source and was now wondering how to finish the installation. I would like to have the binaries in a custom location and not the git source directory. Is there a configure variable that I should have set or can I just move some directories (if so, which?) without breaking the build? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy |
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From: Dmitry S. <sem...@gm...> - 2019-10-15 19:11:35
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Hi Victor, Try to rename your tiff files as 1, 2, 3... Perhaps the problem is in the name. Use few files as a test. Sincerely, Dmitry On October 15, 2019 16:37:40 Victor Manuel Ruiz Arroyo <vr...@ib...> wrote: > Hello, > > > I've changed the pattern even to *.tiff without success. Skipping first > micrographs or selecting just one random micrograph doesn't solve the > problem either. > > > Best > Victor > > > El mar., 15 oct. 2019 a las 16:03, Jose Miguel de la Rosa Trevin > (<del...@gm...>) escribió: > > Hi Victor, > > > Maybe try with a more flexible pattern: > > > Pattern: Pet_*.tiff > > > Or check that your Pet_00000.tiff image is not corrupted. > > > Hope this helps, > Best, > Jose Miguel > > > > > > > On Tue, Oct 15, 2019 at 3:59 PM Victor Manuel Ruiz Arroyo > <vr...@ib...> wrote: > > Hello > > > I'm Victor Ruiz from SBU in Barcelona. I'm working with a new acquisition > of tiff movies but I'm having trouble when importing into Scipion. > > > - Import movies > - Path: > /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/ > > - Pattern: Pet_#####.tiff > > > Error: > Error reading the following images: > /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/Petl_00000.tiff > > > > Using Relion 3.0 I'm able to import and process the movies normally. > > > Am I missing some extra library to read tiff files? > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Victor M. R. A. <vr...@ib...> - 2019-10-15 14:37:30
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Hello, I've changed the pattern even to *.tiff without success. Skipping first micrographs or selecting just one random micrograph doesn't solve the problem either. Best Victor El mar., 15 oct. 2019 a las 16:03, Jose Miguel de la Rosa Trevin (< del...@gm...>) escribió: > Hi Victor, > > Maybe try with a more flexible pattern: > > Pattern: Pet_*.tiff > > Or check that your Pet_00000.tiff image is not corrupted. > > Hope this helps, > Best, > Jose Miguel > > > > On Tue, Oct 15, 2019 at 3:59 PM Victor Manuel Ruiz Arroyo < > vr...@ib...> wrote: > >> Hello >> >> I'm Victor Ruiz from SBU in Barcelona. I'm working with a new acquisition >> of tiff movies but I'm having trouble when importing into Scipion. >> >> - Import movies >> - Path: >> /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/ >> - Pattern: Pet_#####.tiff >> >> Error: >> Error reading the following images: >> /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/Petl_00000.tiff >> >> Using Relion 3.0 I'm able to import and process the movies normally. >> >> Am I missing some extra library to read tiff files? >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Jose M. de la R. T. <del...@gm...> - 2019-10-15 14:02:17
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Hi Victor, Maybe try with a more flexible pattern: Pattern: Pet_*.tiff Or check that your Pet_00000.tiff image is not corrupted. Hope this helps, Best, Jose Miguel On Tue, Oct 15, 2019 at 3:59 PM Victor Manuel Ruiz Arroyo < vr...@ib...> wrote: > Hello > > I'm Victor Ruiz from SBU in Barcelona. I'm working with a new acquisition > of tiff movies but I'm having trouble when importing into Scipion. > > - Import movies > - Path: > /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/ > - Pattern: Pet_#####.tiff > > Error: > Error reading the following images: > /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/Petl_00000.tiff > > Using Relion 3.0 I'm able to import and process the movies normally. > > Am I missing some extra library to read tiff files? > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Victor M. R. A. <vr...@ib...> - 2019-10-15 13:58:45
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Hello I'm Victor Ruiz from SBU in Barcelona. I'm working with a new acquisition of tiff movies but I'm having trouble when importing into Scipion. - Import movies - Path: /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/ - Pattern: Pet_#####.tiff Error: Error reading the following images: /data2/Victor/DATA/2019_Titan_Krios/RAW_DATA/Frames/Petl_00000.tiff Using Relion 3.0 I'm able to import and process the movies normally. Am I missing some extra library to read tiff files? |
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From: 范宏成 <187...@16...> - 2019-10-12 15:39:10
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Dear Carlos, I see. Thank you so much! | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 10/12/2019 21:01，Carlos Oscar S. Sorzano<co...@cn...> wrote： Dear Fan, highres assumes that the particles are phase flipped at extraction and it will use the Xmipp CTF parameters for the CTF correction. I have never used it outside these conditions. If you drop all the columns referring to CTF (especially the defocus), you will fool the protocol making it think that they are coming from simulated data (they also lack of defocus parameters) and it will not do any CTF correction. I don't know what will be the result, but it will be interesting to know. Kind regards, Carlos Oscar El 11/10/2019 a las 17:31, 范宏成 escribió: Dear Colleagues, I got polished(shiny) particles from relion 3.0. I want to import scipion to try the protocol Highres. The warning said: Highres work on phase flipped particles. So I need to re-extract particles using xmipp extract particles protocols . I am afraid the particles are no longer shiny particles. So How to solve it? Thank you! Fan Hongcheng | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Carlos O. S. S. <co...@cn...> - 2019-10-12 15:01:29
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Dear Fan, highres assumes that the particles are phase flipped at extraction and it will use the Xmipp CTF parameters for the CTF correction. I have never used it outside these conditions. If you drop all the columns referring to CTF (especially the defocus), you will fool the protocol making it think that they are coming from simulated data (they also lack of defocus parameters) and it will not do any CTF correction. I don't know what will be the result, but it will be interesting to know. Kind regards, Carlos Oscar El 11/10/2019 a las 17:31, 范宏成 escribió: > Dear Colleagues, > I got polished(shiny) particles from relion 3.0. I want to import > scipion to try the protocol Highres. The warning said: Highres work on > phase flipped particles. So I need to re-extract particles using > xmipp extract particles protocols . I am afraid the particles are no > longer shiny particles. So How to solve it? Thank you! > > Fan Hongcheng > > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&ftlId=1&iconUrl=http%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> > > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> > 定制 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: 范宏成 <187...@16...> - 2019-10-11 15:31:17
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Dear Colleagues, I got polished(shiny) particles from relion 3.0. I want to import scipion to try the protocol Highres. The warning said: Highres work on phase flipped particles. So I need to re-extract particles using xmipp extract particles protocols . I am afraid the particles are no longer shiny particles. So How to solve it? Thank you! Fan Hongcheng | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 |
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From: Dmitry S. <sem...@gm...> - 2019-10-02 12:49:38
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Dear Pablo, Personally I wasn't aware of them. I guess you are referring to this: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies#Anchor-BioUnit Yes, exactly. It is useful when you want to upload initial reference and you have the pdb that is not always the biological assembly but just a piece of the required model. Of course the walk around is that you download the biological assembly file from the pdb website – open in chimera – combine it in 1 pdb and then use the same SCIPION protocol but as import file option. Thank you! Sincerely, Dmitry From: Pablo Conesa <pc...@cn...> Reply to: Mailing list for Scipion users <sci...@li...> Date: Wednesday, 2. October 2019 at 14:11 To: <sci...@li...> Subject: Re: [scipion-users] Small question Hi Dimitry, it is clear now what are you referring to...thanks.... Personally I wasn't aware of them. I guess you are referring to this: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies#Anchor-BioUnit I guess that meanwhile we decide to include this.....There is a way to ask Chimera to do it and then import it in Scipion? On 2/10/19 12:11, Dmitry Semchonok wrote: Dear Marta, This the protocol in SCIPION 2 --> 3D -->Initial Volume --> xmipp3 – convert a PDB Inside this protocol there are the following options – Retrieve PDB from id; object; file So what would be useful if we can have one more button as it in Chimera saying id biounit – and it is loading not a single/part of the molecule but the full biological unit Thank you! Sincerely, Dmitry On 02.10.19, 09:18, "Marta Martinez" <mm...@cn...> wrote: Hi Dmitry, please, what Scipion protocol are you talking about? Regards: MARTA Dear colleagues, Small question When we import the PDB (in the initial volume tab) it is good to have PDB assembly option or as it in chimera – PDB biounit. Is that possible? Sincerely, Dmitry -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mm...@cn... _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2019-10-02 12:10:55
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Hi Dimitry, it is clear now what are you referring to...thanks.... Personally I wasn't aware of them. I guess you are referring to this: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies#Anchor-BioUnit I guess that meanwhile we decide to include this.....There is a way to ask Chimera to do it and then import it in Scipion? On 2/10/19 12:11, Dmitry Semchonok wrote: > Dear Marta, > > This the protocol in SCIPION 2 --> 3D -->Initial Volume --> xmipp3 – convert a PDB > > > Inside this protocol there are the following options – Retrieve PDB from id; object; file > > So what would be useful if we can have one more button as it in Chimera saying id biounit – and it is loading not a single/part of the molecule but the full biological unit > > Thank you! > > Sincerely, > Dmitry > > > > On 02.10.19, 09:18, "Marta Martinez" <mm...@cn...> wrote: > > > Hi Dmitry, > please, what Scipion protocol are you talking about? > Regards: MARTA > > > > > Dear colleagues, > > > > Small question > > When we import the PDB (in the initial volume tab) it is good to have > PDB assembly option or as it in chimera – PDB biounit. > > Is that possible? > > > > Sincerely, > > Dmitry > > > > -- > Marta Martinez Gonzalez > > Biocomputing Unit (Lab B13) > National Center for Biotechnology-CSIC > Darwin, 3. Campus de la Universidad Autonoma de Madrid > 28049 Madrid. Spain > Tel:+34 915854510 Fax:+34 913720112 > E-mail: mm...@cn... > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <sem...@gm...> - 2019-10-02 10:11:16
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Dear Marta,
This the protocol in SCIPION 2 --> 3D -->Initial Volume --> xmipp3 – convert a PDB
Inside this protocol there are the following options – Retrieve PDB from id; object; file
So what would be useful if we can have one more button as it in Chimera saying id biounit – and it is loading not a single/part of the molecule but the full biological unit
Thank you!
Sincerely,
Dmitry
On 02.10.19, 09:18, "Marta Martinez" <mm...@cn...> wrote:
Hi Dmitry,
please, what Scipion protocol are you talking about?
Regards: MARTA
Dear colleagues,
Small question
When we import the PDB (in the initial volume tab) it is good to have
PDB assembly option or as it in chimera – PDB biounit.
Is that possible?
Sincerely,
Dmitry
--
Marta Martinez Gonzalez
Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mm...@cn...
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
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From: Marta M. <mm...@cn...> - 2019-10-02 07:18:24
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Hi Dmitry, please, what Scipion protocol are you talking about? Regards: MARTA Dear colleagues, Small question When we import the PDB (in the initial volume tab) it is good to have PDB assembly option or as it in chimera – PDB biounit. Is that possible? Sincerely, Dmitry -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mm...@cn... |
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From: Dmitry S. <sem...@gm...> - 2019-10-01 12:44:03
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Dear colleagues, Small question When we import the PDB (in the initial volume tab) it is good to have PDB assembly option or as it in chimera – PDB biounit. Is that possible? Sincerely, Dmitry |
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From: Elad B. <ela...@va...> - 2019-09-30 13:59:20
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Hi Victor, What you need to do is extract the 'good' particles from your last 2D\3D\refine job using 'scipion - extract coordinates' and then re-extract the particle with full size. Best, EB On Mon, Sep 30, 2019 at 6:05 AM Juha Huiskonen <juh...@he...> wrote: > > Hi Victor, > > The protocols are called 'scipion - extract coordinates' and 'scipion - > assign alignment'. > > You can find them under All protocols, or give control+F to search for > them. > > Best wishes, > Juha > > > > > On Mon, Sep 30, 2019 at 1:00 PM Victor Manuel Ruiz Arroyo < > vr...@ib...> wrote: > >> Hello, >> >> I'm Victor Ruiz, PhD student at SBU in Barcelona, Spain. >> I'm writing here because I'm performing some 3D refinements with my >> current subset of binned particles, now I've reached nyquist, I want for >> perform the refinements at full mag but I cannot find out where is the >> option that is available in relion-particle extraction to re-extract my >> subset of particles maintaining the refined angles. >> >> Thanks in advance! >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C2ff3b599920a4f96cde608d745976dcf%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637054389001369264&sdata=8%2FsLdTND4Kha44ZSLg4Yo9xPGWEy5ucJEciXwNUsTSA%3D&reserved=0> >> > -- ________________________________ Elad Binshtein, Ph.D. Cryo-EM specialist - Senior Staff Scientist Center for Structure Biology (CSB) MCN Room 1207 Vanderbilt University Nashville, TN Office: +1-615-322-4671 Mobile: +1-615-481-4408 https://www.linkedin.com/in/elad-binshtein-6bb89428/ E-Mail: ela...@va... <el...@gm...> twitter @EladBinshtein ________________________________ |
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From: Juha H. <juh...@he...> - 2019-09-30 11:06:32
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Hi Victor, The protocols are called 'scipion - extract coordinates' and 'scipion - assign alignment'. You can find them under All protocols, or give control+F to search for them. Best wishes, Juha On Mon, Sep 30, 2019 at 1:00 PM Victor Manuel Ruiz Arroyo < vr...@ib...> wrote: > Hello, > > I'm Victor Ruiz, PhD student at SBU in Barcelona, Spain. > I'm writing here because I'm performing some 3D refinements with my > current subset of binned particles, now I've reached nyquist, I want for > perform the refinements at full mag but I cannot find out where is the > option that is available in relion-particle extraction to re-extract my > subset of particles maintaining the refined angles. > > Thanks in advance! > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Victor M. R. A. <vr...@ib...> - 2019-09-30 10:58:34
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Hello, I'm Victor Ruiz, PhD student at SBU in Barcelona, Spain. I'm writing here because I'm performing some 3D refinements with my current subset of binned particles, now I've reached nyquist, I want for perform the refinements at full mag but I cannot find out where is the option that is available in relion-particle extraction to re-extract my subset of particles maintaining the refined angles. Thanks in advance! |
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