Menu
▾
▴
scipion-users — Mailing list for Scipion users
You can subscribe to this list here.
| 2016 |
Jan
(2) |
Feb
(13) |
Mar
(9) |
Apr
(4) |
May
(5) |
Jun
(2) |
Jul
(8) |
Aug
(3) |
Sep
(25) |
Oct
(7) |
Nov
(49) |
Dec
(15) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 |
Jan
(24) |
Feb
(36) |
Mar
(53) |
Apr
(44) |
May
(37) |
Jun
(34) |
Jul
(12) |
Aug
(15) |
Sep
(14) |
Oct
(9) |
Nov
(9) |
Dec
(7) |
| 2018 |
Jan
(16) |
Feb
(9) |
Mar
(27) |
Apr
(39) |
May
(8) |
Jun
(24) |
Jul
(22) |
Aug
(11) |
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2019 |
Jan
(4) |
Feb
(5) |
Mar
|
Apr
(1) |
May
(21) |
Jun
(13) |
Jul
(31) |
Aug
(22) |
Sep
(9) |
Oct
(19) |
Nov
(24) |
Dec
(12) |
| 2020 |
Jan
(30) |
Feb
(12) |
Mar
(16) |
Apr
(4) |
May
(37) |
Jun
(17) |
Jul
(19) |
Aug
(15) |
Sep
(26) |
Oct
(84) |
Nov
(64) |
Dec
(55) |
| 2021 |
Jan
(18) |
Feb
(58) |
Mar
(26) |
Apr
(88) |
May
(51) |
Jun
(36) |
Jul
(31) |
Aug
(37) |
Sep
(79) |
Oct
(15) |
Nov
(29) |
Dec
(8) |
| 2022 |
Jan
(5) |
Feb
(8) |
Mar
(29) |
Apr
(21) |
May
(11) |
Jun
(11) |
Jul
(18) |
Aug
(16) |
Sep
(6) |
Oct
(10) |
Nov
(23) |
Dec
(1) |
| 2023 |
Jan
(18) |
Feb
|
Mar
(4) |
Apr
|
May
(3) |
Jun
(10) |
Jul
(1) |
Aug
|
Sep
|
Oct
(1) |
Nov
(3) |
Dec
(5) |
| 2024 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2025 |
Jan
(1) |
Feb
|
Mar
|
Apr
(5) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Dmitry S. <sem...@gm...> - 2016-11-22 10:55:41
|
Dear colleagues, 1 more question How do you use the *protocol grigoriefflab - unblur*? After the *movie alignment protocol*? How important is to use this protocol? Isn't the particle polishing will in a way do the same? Thank you Sincerely, Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2016-11-22 10:04:15
|
Dear colleagues, I used protocol xmipp3 - movie alignment but only cross-correlation correction. But now I would like to add optical correction. Is there a way to redo this step? I already processed till the final 3d model.... Also I would like to incert xmipp - ctf extimation protocol inbetween grigotieflab and particle picking Is that any possible? Sincerely, Dmitry |
|
From: Grigory S. <sha...@gm...> - 2016-11-21 18:43:15
|
Hello Dmitry, May I ask why are you doing this instead of importing coordinates? On Nov 21, 2016 21:31, "Dmitry Semchonok" <sem...@gm...> wrote: > > Dear colleagues, > > > We still have an issue with creating coordinates file. > > > > Placing the *.pos files in the extra directory still doesn't make the protocol xmipp3 - manual picking to see the coordinates. Of course this won't work. > > > > Probably we are doing something wrong. > > Please see the example of *.pos file we are using > > ======================================================================== > > Name: > > FoilHole_25566402_Data_25564800_25564801_20160825_2249-21269-stack_aligned.pos > > > > Inside: > > # XMIPP_STAR_1 * > > # > > data_header > > loop_ > > _pickingMicrographState > > _autopickPercent > > _cost > > Manual 0 0.0 > > data_particles > > loop_ > > _xcoor > > _ycoor > > 3450 2670 > > 2944 2883 > > 3448 984 > > 1528 808 > > 1172 3372 > > 3596 364 > > > > ==================================================================== > > I would like to know what files are essential to put in the XmippProtParticlePicking folder: > > > > *.pos? > > Coordinates.sqlite? > > > Thank you! > > > Sincerely, > > Dmitry > > > ------------------------------------------------------------------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Dmitry S. <sem...@gm...> - 2016-11-21 18:31:21
|
Dear colleagues,
We still have an issue with creating coordinates file.
Placing the *.pos files in the *extra* directory still doesn't make the
protocol *xmipp3 - manual picking* to see the coordinates.
Probably we are doing something wrong.
Please see the example of *.pos file we are using
========================================================================
*Name: *
FoilHole_25566402_Data_25564800_25564801_20160825_2249-21269-stack_aligned.pos
*Inside:*
# XMIPP_STAR_1 *
#
data_header
loop_
_pickingMicrographState
_autopickPercent
_cost
Manual 0 0.0
data_particles
loop_
_xcoor
_ycoor
3450 2670
2944 2883
3448 984
1528 808
1172 3372
3596 364
====================================================================
I would like to know what files are essential to put in the
*XmippProtParticlePicking* folder:
*.pos?
Coordinates.sqlite?
Thank you!
Sincerely,
Dmitry
|
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-17 16:15:13
|
Hi Dmitry, Just go to the last excuted run in Runs/ folder and copy the logs/run.db file into the project.sqlite. This should restore the project database to the state when you launched the protocols. Bests, Jose Miguel On Thu, Nov 17, 2016 at 5:12 PM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I got into trouble making the backup with rsync. > > The *current project.sqlite* file was* substituted* with an* old > project.sqlite*. > > > The good thing is that the all steps that I did stay as they were in the > Run folder (with correspondent id .....) > > Is there a way to *regenerate* the *project.sqlite* file based on the > files in the *Run* folder? > > > If yes then how? > > > Thank you. > > Sincerely, > Dmitry > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Dmitry S. <sem...@gm...> - 2016-11-17 16:12:15
|
Dear colleagues, I got into trouble making the backup with rsync. The *current project.sqlite* file was* substituted* with an* old project.sqlite*. The good thing is that the all steps that I did stay as they were in the Run folder (with correspondent id .....) Is there a way to *regenerate* the *project.sqlite* file based on the files in the *Run* folder? If yes then how? Thank you. Sincerely, Dmitry |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-16 11:09:02
|
Dear Dmitry, This is a great idea! We would include this in the Scipion wish-list. Thanks for your feedback, Jose Miguel On Wed, Nov 16, 2016 at 11:54 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > A small proposition about Protocol* scipion – extract coordinates* > > > > It would be very helpful to mark with another color the picked particles > that belongs to any other classes. > > > > When you use *scipion – extract coordinates* protocol you browse through > every micrograph aiming to center the particle etc. > > > Great if we could see the other picked particles that belongs to the > other classes – doesn’t matter which classes. So that we can find the > particles that were not being picked and were overlooked. > > > Please see the possible example in the attachment. > > > > Sincerely, > > Dmitry > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Dmitry S. <sem...@gm...> - 2016-11-16 10:54:46
|
Dear colleagues, A small proposition about Protocol* scipion – extract coordinates* It would be very helpful to mark with another color the picked particles that belongs to any other classes. When you use *scipion – extract coordinates* protocol you browse through every micrograph aiming to center the particle etc. Great if we could see the other picked particles that belongs to the other classes – doesn’t matter which classes. So that we can find the particles that were not being picked and were overlooked. Please see the possible example in the attachment. Sincerely, Dmitry |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-14 22:24:54
|
Hi Dmitry, The particles that are you trying to transfer have been picking also in Scipion/Xmipp? There is a protocols where you can import coordinates in a given project in Scipion. Moreover, in the Xmipp-Picking GUI, you can also go to File -> Import Coordinates and select a file for the selected micrograph or a folder (where the files should be names as the micrographs without extension) and import into the current picking job. Hope this helps, Bests, Jose Miguel On Sat, Nov 12, 2016 at 11:33 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I'm trying to transfer the selected picked particles into the > *XmippProtParticlePicking/* > > We created *.pos files with required coordinates and file names. > > I transferred *.pos files into *extra* folder but the protocol *did not > picked* those coordinate positions. > > Am I missing something? > *What are the other files required?* > > > Thank you. > > > Sincerely, > Dmitry > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-14 22:18:14
|
Hi Simone, The issues with the connectivity at our institute could be causing the problem as Pablo suggest. Nonetheless, I think I have seen those errors in other circumstances. First, when building Scipion from source code (from git) it build Xmipp by default and this error seems related to Java bindings, so be sure that Java jdk is properly set and everything is compiling properly without any extra EM package (just scipion install -j 5). When installing other EM packages, make sure to use the *--no-xmipp *option as stated in the How To Install wiki page. It will try to install other EM packages without building Xmipp, we are considering to change this behavior in a future and do not install Xmipp by default always. Please let us know if you manage to get Scipion properly installed with other EM packages and do not hesitate to contact us for further assistance. Bests, Jose Miguel On Mon, Nov 14, 2016 at 8:13 PM, Simone PELLEGRINO <pel...@ig...> wrote: > Hello Pablo, > > > ok that sounds like the source of the problem. We will try to keep trying > and hopefully getting some connection back soon. > > > We followed the link you sent to me, so I think we are in the right way. > > > Best > > Simone > > > > Dr. Simone Pellegrino > Integrated Structural Biology > Marat Yusupov's team > I.G.B.M.C. > 1, rue Laurent Fries > BP 10142 - 67404 Illkirch CEDEX > Tel: +33 (0)3 88 65 33 52 > > E.mail: sim...@ig... > ------------------------------ > *From:* Pablo Conesa <pc...@cn...> > *Sent:* 14 November 2016 18:47 > *To:* Simone PELLEGRINO; sci...@li... > *Subject:* Re: [scipion-users] Problems with installing EM packages in > Scipion from git > > > Dear Simone! > > > Today we've been going through a major network upgrade in our institute. > And will last for s few days. > > > This means that we will experience short disconnection periods. This will > explain those error you where getting, assuming you were trying today. > > > If so, keep trying, now for example we have connectivity, hence this email. > > One question, Have you gone through the "Github" installation > instructions? See this > <https://github.com/I2PC/scipion/wiki/How-to-Install> > > Let us know how it goes, > > > All the best, Pablo. > > > > On 14/11/16 16:05, Simone PELLEGRINO wrote: > > Dear all, > > > we are experiencing problems in installing the single EM packages from the > version of Scipion obtained from the git. The errors are the following: > > > ctffind4: > g++ -o software/em/xmipp/lib/libXmippJNI.so -shared > software/em/xmipp/libraries/bindings/java/xmipp_Pic > kingClassifier.os software/em/xmipp/libraries/bindings/java/xmipp_ProgTomographAlignment.os > software/em > /xmipp/libraries/bindings/java/xmipp_Program.os > software/em/xmipp/libraries/bindings/java/xmipp_CTFDesc > ription.os software/em/xmipp/libraries/bindings/java/xmipp_MDRow.os > software/em/xmipp/libraries/binding > s/java/xmipp_Filename.os software/em/xmipp/libraries/bindings/java/xmipp_ImageGeneric.os > software/em/xm > ipp/libraries/bindings/java/xmipp_ExceptionsHandler.os > software/em/xmipp/libraries/bindings/java/xmipp_ > Aux.os software/em/xmipp/libraries/bindings/java/xmipp_MetaData.os > software/em/xmipp/libraries/bindings > /java/xmipp_Projection.os software/em/xmipp/libraries/bindings/java/xmipp_TiltPairAligner.os > -Lsoftware > /em/xmipp/lib -Lsoftware/lib -lpthread -lXmippData -lXmippRecons > -lXmippClassif -lXmippBilib > Install file: "software/em/xmipp/lib/libXmippJNI.so" as > "software/lib/libXmippJNI.so" > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > frealign: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > motioncorr: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > resmap: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > spider: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > unblur: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > eman2.12: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > > > Does anyone know why please? With the version obtained from the webpage it > does install everything without any problem. > > Thank you very much for helping > > > Best > > Simone > > > Dr. Simone Pellegrino > Integrated Structural Biology > Marat Yusupov's team > I.G.B.M.C. > 1, rue Laurent Fries > BP 10142 - 67404 Illkirch CEDEX > Tel: +33 (0)3 88 65 33 52 > > E.mail: sim...@ig... > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Simone P. <pel...@ig...> - 2016-11-14 19:49:15
|
Hello Pablo, ok that sounds like the source of the problem. We will try to keep trying and hopefully getting some connection back soon. We followed the link you sent to me, so I think we are in the right way. Best Simone Dr. Simone Pellegrino Integrated Structural Biology Marat Yusupov's team I.G.B.M.C. 1, rue Laurent Fries BP 10142 - 67404 Illkirch CEDEX Tel: +33 (0)3 88 65 33 52 E.mail: sim...@ig... ________________________________ From: Pablo Conesa <pc...@cn...> Sent: 14 November 2016 18:47 To: Simone PELLEGRINO; sci...@li... Subject: Re: [scipion-users] Problems with installing EM packages in Scipion from git Dear Simone! Today we've been going through a major network upgrade in our institute. And will last for s few days. This means that we will experience short disconnection periods. This will explain those error you where getting, assuming you were trying today. If so, keep trying, now for example we have connectivity, hence this email. One question, Have you gone through the "Github" installation instructions? See this<https://github.com/I2PC/scipion/wiki/How-to-Install> Let us know how it goes, All the best, Pablo. On 14/11/16 16:05, Simone PELLEGRINO wrote: Dear all, we are experiencing problems in installing the single EM packages from the version of Scipion obtained from the git. The errors are the following: ctffind4: g++ -o software/em/xmipp/lib/libXmippJNI.so -shared software/em/xmipp/libraries/bindings/java/xmipp_Pic kingClassifier.os software/em/xmipp/libraries/bindings/java/xmipp_ProgTomographAlignment.os software/em /xmipp/libraries/bindings/java/xmipp_Program.os software/em/xmipp/libraries/bindings/java/xmipp_CTFDesc ription.os software/em/xmipp/libraries/bindings/java/xmipp_MDRow.os software/em/xmipp/libraries/binding s/java/xmipp_Filename.os software/em/xmipp/libraries/bindings/java/xmipp_ImageGeneric.os software/em/xm ipp/libraries/bindings/java/xmipp_ExceptionsHandler.os software/em/xmipp/libraries/bindings/java/xmipp_ Aux.os software/em/xmipp/libraries/bindings/java/xmipp_MetaData.os software/em/xmipp/libraries/bindings /java/xmipp_Projection.os software/em/xmipp/libraries/bindings/java/xmipp_TiltPairAligner.os -Lsoftware /em/xmipp/lib -Lsoftware/lib -lpthread -lXmippData -lXmippRecons -lXmippClassif -lXmippBilib Install file: "software/em/xmipp/lib/libXmippJNI.so" as "software/lib/libXmippJNI.so" scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. frealign: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. motioncorr: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. resmap: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. spider: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. unblur: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. eman2.12: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. scons: building terminated because of errors. Does anyone know why please? With the version obtained from the webpage it does install everything without any problem. Thank you very much for helping Best Simone? Dr. Simone Pellegrino Integrated Structural Biology Marat Yusupov's team I.G.B.M.C. 1, rue Laurent Fries BP 10142 - 67404 Illkirch CEDEX Tel: +33 (0)3 88 65 33 52 E.mail: sim...@ig...<mailto:sim...@ig...> ------------------------------------------------------------------------------ _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Pablo C. <pc...@cn...> - 2016-11-14 17:47:27
|
Dear Simone! Today we've been going through a major network upgrade in our institute. And will last for s few days. This means that we will experience short disconnection periods. This will explain those error you where getting, assuming you were trying today. If so, keep trying, now for example we have connectivity, hence this email. One question, Have you gone through the "Github" installation instructions? See this <https://github.com/I2PC/scipion/wiki/How-to-Install> Let us know how it goes, All the best, Pablo. On 14/11/16 16:05, Simone PELLEGRINO wrote: > > Dear all, > > > we are experiencing problems in installing the single EM packages from > the version of Scipion obtained from the git. The errors are the > following: > > > ctffind4: > g++ -o software/em/xmipp/lib/libXmippJNI.so -shared > software/em/xmipp/libraries/bindings/java/xmipp_Pic > kingClassifier.os > software/em/xmipp/libraries/bindings/java/xmipp_ProgTomographAlignment.os > software/em > /xmipp/libraries/bindings/java/xmipp_Program.os > software/em/xmipp/libraries/bindings/java/xmipp_CTFDesc > ription.os software/em/xmipp/libraries/bindings/java/xmipp_MDRow.os > software/em/xmipp/libraries/binding > s/java/xmipp_Filename.os > software/em/xmipp/libraries/bindings/java/xmipp_ImageGeneric.os > software/em/xm > ipp/libraries/bindings/java/xmipp_ExceptionsHandler.os > software/em/xmipp/libraries/bindings/java/xmipp_ > Aux.os software/em/xmipp/libraries/bindings/java/xmipp_MetaData.os > software/em/xmipp/libraries/bindings > /java/xmipp_Projection.os > software/em/xmipp/libraries/bindings/java/xmipp_TiltPairAligner.os > -Lsoftware > /em/xmipp/lib -Lsoftware/lib -lpthread -lXmippData -lXmippRecons > -lXmippClassif -lXmippBilib > Install file: "software/em/xmipp/lib/libXmippJNI.so" as > "software/lib/libXmippJNI.so" > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > frealign: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > motioncorr: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > resmap: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > spider: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > unblur: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > eman2.12: > scons: *** [software/em/xmipp/external/imagej/ij.jar] Source > `software/em/xmipp/external/imagej.tgz' no > t found, needed by target `software/em/xmipp/external/imagej/ij.jar'. > scons: building terminated because of errors. > > > > Does anyone know why please? With the version obtained from the > webpage it does install everything without any problem. > > Thank you very much for helping > > > Best > > Simone > > > Dr. Simone Pellegrino > Integrated Structural Biology > Marat Yusupov's team > I.G.B.M.C. > 1, rue Laurent Fries > BP 10142 - 67404 Illkirch CEDEX > Tel: +33 (0)3 88 65 33 52 > > E.mail: sim...@ig... > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Simone P. <pel...@ig...> - 2016-11-14 16:38:41
|
Dear all,
we are experiencing problems in installing the single EM packages from the version of Scipion obtained from the git. The errors are the following:
ctffind4:
g++ -o software/em/xmipp/lib/libXmippJNI.so -shared software/em/xmipp/libraries/bindings/java/xmipp_Pic
kingClassifier.os software/em/xmipp/libraries/bindings/java/xmipp_ProgTomographAlignment.os software/em
/xmipp/libraries/bindings/java/xmipp_Program.os software/em/xmipp/libraries/bindings/java/xmipp_CTFDesc
ription.os software/em/xmipp/libraries/bindings/java/xmipp_MDRow.os software/em/xmipp/libraries/binding
s/java/xmipp_Filename.os software/em/xmipp/libraries/bindings/java/xmipp_ImageGeneric.os software/em/xm
ipp/libraries/bindings/java/xmipp_ExceptionsHandler.os software/em/xmipp/libraries/bindings/java/xmipp_
Aux.os software/em/xmipp/libraries/bindings/java/xmipp_MetaData.os software/em/xmipp/libraries/bindings
/java/xmipp_Projection.os software/em/xmipp/libraries/bindings/java/xmipp_TiltPairAligner.os -Lsoftware
/em/xmipp/lib -Lsoftware/lib -lpthread -lXmippData -lXmippRecons -lXmippClassif -lXmippBilib
Install file: "software/em/xmipp/lib/libXmippJNI.so" as "software/lib/libXmippJNI.so"
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
frealign:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
motioncorr:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
resmap:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
spider:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
unblur:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
eman2.12:
scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' no
t found, needed by target `software/em/xmipp/external/imagej/ij.jar'.
scons: building terminated because of errors.
Does anyone know why please? With the version obtained from the webpage it does install everything without any problem.
Thank you very much for helping
Best
Simone?
Dr. Simone Pellegrino
Integrated Structural Biology
Marat Yusupov's team
I.G.B.M.C.
1, rue Laurent Fries
BP 10142 - 67404 Illkirch CEDEX
Tel: +33 (0)3 88 65 33 52
E.mail: sim...@ig...
|
|
From: Dmitry S. <sem...@gm...> - 2016-11-12 10:34:06
|
Dear colleagues, I'm trying to transfer the selected picked particles into the *XmippProtParticlePicking/* We created *.pos files with required coordinates and file names. I transferred *.pos files into *extra* folder but the protocol *did not picked* those coordinate positions. Am I missing something? *What are the other files required?* Thank you. Sincerely, Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2016-11-10 14:14:51
|
Dear colleagues,
the new issue with exporting/importing the coordinates.
*What I have*==============================================================
I worked with it separately: Grid1 ----Motion correction
----CTF-----Particle picking---
Grid2 ----Motion correction
----CTF-----Particle picking---
------------------------------///------------------------------------------
After I combined all autopicked particles in 1 file.
With this file I run till the end - 3d model (postprocessing).
As a result I got ~ 16000 good particles.
===============================================================
*What I want*
*===============================================================*
My idea is to work again with these good ~16000 particles.
>From info in particles file you can see the correspondent mrc files they
refer and create a "new" set of mrc.
So now I have the "new" set of mrc that I start processing from the
beginning (instead og Grid1..Grid2..)
The problem I faced is
to get the coordinate files for these ~16000 particles
to apply it for the "new" set of mrc that might contain these particles.
*So how can I*
get the 1 coordinate file where all my 16000 particles are listed and
to apply it to the "new" mrc set and
be able to move a boxes if now they are not centered.
I tried *xmipp - extract coordinates* protocol.
It works with old Grid1 Grid2......mrc sets but not with a "new" mrc one.
Thank you.
Sincerely,
Dmitry
|
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-10 11:03:28
|
Dear Dmitry, We have detected a bug related to sorting columns (after show then from Tools -> Columns..). We have fixed it and testing...when ready we will let you know. Cheers, Jose Miguel. On Thu, Nov 10, 2016 at 11:53 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > > If in *metadata ctfs.sqlite* file you will select some new columns > (Tools-->Columns--> …..) > > > > And if you sort the pictures based on the new added columns it becomes not > possible after to sort by any other columns. The sorting stuck only to that > 1 column. > > > > Is it a bug? > > > Sincerely, > > Dmitry > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Pablo C. <pc...@cn...> - 2016-11-10 11:03:21
|
Dear Dmitry. Yes, it is a bug, hard to hide that under a "feature", ;-). We've just fixed it and will be released with the new version. Thanks for reporting, Pablo. On 10/11/16 11:53, Dmitry Semchonok wrote: > > Dear colleagues, > > > If in *metadata ctfs.sqlite* file you will select some new columns > (Tools-->Columns--> …..) > > And if you sort the pictures based on the new added columns it becomes > not possible after to sort by any other columns. The sorting stuck > only to that 1 column. > > > > Is it a bug? > > > Sincerely, > > Dmitry > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry S. <sem...@gm...> - 2016-11-10 10:53:11
|
Dear colleagues, If in *metadata ctfs.sqlite* file you will select some new columns (Tools-->Columns--> …..) And if you sort the pictures based on the new added columns it becomes not possible after to sort by any other columns. The sorting stuck only to that 1 column. Is it a bug? Sincerely, Dmitry |
|
From: Jose M. de la R. T. <del...@gm...> - 2016-11-09 13:40:09
|
Thanks for you suggestion Dmitry. I agree with you that would be convenient to sort by the number of particles, or even provide an option in the protocol to exclude the micrographs with zero particles. Another feature that we have been talked about (but not implemented yet), is to apply the possible shifts of the particles to extract better coordinates positions. Maybe this also leverage the need to re-center them. Cheers, Jose Miguel. On Wed, Nov 9, 2016 at 2:05 PM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > Some options for the improvements: > > > Protocol *scipion – extract coordinates* > > > Sometimes you need to re-pick particles in order to pick the center of it > etc. > > > It can be handy to be able to: > > sort the particles by number (in the column *Particles* – protocol *scipion > – extract coordinates*) – that saves time browsing through the all > dataset that sometimes has “0” of particles you need through many images(please > see the attachment) > > > > Sincerely, > > Dmitry > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Dmitry S. <sem...@gm...> - 2016-11-09 13:05:09
|
Dear colleagues, Some options for the improvements: Protocol *scipion – extract coordinates* Sometimes you need to re-pick particles in order to pick the center of it etc. It can be handy to be able to: sort the particles by number (in the column *Particles* – protocol *scipion – extract coordinates*) – that saves time browsing through the all dataset that sometimes has “0” of particles you need through many images(please see the attachment) Sincerely, Dmitry |
|
From: Carlos O. S. <co...@cn...> - 2016-11-08 21:03:10
|
Dear Dmitry, thank you for the update. In the old days this used to be a common problem because in the same computer there was normally several MPI versions. With current Linux distributions, it seems this problem is less common. Kind regards, Carlos Oscar On 11/08/16 14:41, Dmitry Semchonok wrote: > Dear colleagues, > > the reason of my problem was that: > > some XMIPP executables are linked against two different MPI libraries, > one that is correct and the other is this incorrect libmpi.so.1 (which > does not even seem to exist). > > The software was rebuilt. > > > Now the *xmipp3-reconstruct significant* works. > > Thank you! > > Sincerely, > Dmitry > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > _______________________________________________ > 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://biocomp.cnb.csic.es 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 ------------------------------------------------------------------------ |
|
From: Dmitry S. <sem...@gm...> - 2016-11-08 13:41:19
|
Dear colleagues, the reason of my problem was that: some XMIPP executables are linked against two different MPI libraries, one that is correct and the other is this incorrect libmpi.so.1 (which does not even seem to exist). The software was rebuilt. Now the *xmipp3-reconstruct significant* works. Thank you! Sincerely, Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2016-11-08 09:26:44
|
Dear colleagues, I try the correct parameters for *xmipp3 - reconstruct significant *that Carlos Oscar suggested (*.jpeg in the attachment). (I use d6 symmetry protein) Now the program gives another error :) In the attachment please see the log files. Any ideas? may be something in the *.config file to check? Sincerely, Dmitry |
|
From: Carlos O. S. <co...@cn...> - 2016-11-07 18:36:16
|
Dear all, reconstruct_significant internally multiplies the significance by the symmetry number (this is done to let symmetric particles to have the same number of chances as non-symmetric). If you start with 0.2, then 0.2*12=2.4>1, which is not a valid significance value. In this case, you may want to start with 0.98 to 0.999. Kind regards, Carlos Oscar On 07/11/2016 16:48, Grigory Sharov wrote: > Hi Dmitry, > > sorry I didn't look carefully first time. > > I guess Carlos Oscar can help you with the error with alpha values in > significant protocol. I have attached the log files you sent me. > > [32mxmipp_reconstruct_significant -i > Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd > --sym d6 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt > 90.000000 --maxShift -1.000000 --dontReconstruct --angDistance > 10.000000 --useImed --odir > Runs/001412_XmippProtReconstructSignificant/tmp/iter001 --alpha0 > 0.200000 --alphaF 0.200000 --numberOfVolumes 1 [0m > Setting iterations to 1 because of --dontReconstruct > Input metadata : > Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd > Output directory : > Runs/001412_XmippProtReconstructSignificant/tmp/iter001 > Initial significance : 0.2 > Final significance : 0.2 > Number of iterations : 1 > Keep intermediate volumes : 0 > Angular sampling : 5 > Maximum shift : -1 > Minimum tilt : 0 > Maximum tilt : 90 > Use Imed : 1 > Angular distance : 10 > Apply Fisher : 0 > Reconstruct : 0 > useForValidation : 0 > Symmetry for projections : d6 > Number of volumes : 1 > [1;31mXMIPP_ERROR 2: Incorrect argument received [0m > [1;31m [1;31mAlpha values are too large: reduce the error such > that the error times the symmetry number is smaller than 1 [0m [0m > [1;31mFile: > software/em/xmipp/libraries/reconstruction/reconstruct_significant.cpp > line: 737 > > > > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > Institute of Genetics and Molecular and Cellular Biology > Integrated Structural Biology Department (CBI) > 1, rue Laurent Fries > 67404 Illkirch, France > tel. 03 69 48 51 00 > e-mail: sh...@ig... <mailto:sh...@ig...> > > On Mon, Nov 7, 2016 at 4:30 PM, Carlos Oscar Sorzano <co...@cn... > <mailto:co...@cn...>> wrote: > > Dear Dmitry, > > as Grigori says, only with these errors it is hard to say what is > going on, is there any other error message? > > Kind regards, Carlos Oscar > > > On 11/07/16 13:22, Dmitry Semchonok wrote: >> Dear colleagues, >> >> I have a problem with running >> >> xmipp3 - ctf_correct_wiener2d >> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: >> >> xmipp3 - reconstruct significant >> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: >> >> >> I faced the following errors: >> >> xmipp3 - ctf_correct_wiener2d >> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: >> Protocol failed: Command 'srun `which >> xmipp_mpi_ctf_correct_wiener2d` -i >> Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o >> Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk >> --save_metadata_stack >> Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.xmd >> --pad 2 --wc -1.0 --sampling_rate 2.24' returned non-zero exit >> status 127 >> >> >> xmipp3 - reconstruct significant >> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> >> Protocol failed: Command 'srun `which >> xmipp_mpi_reconstruct_significant` -i >> Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd >> --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt >> 90.000000 --maxShift -1.000000 --dontReconstruct --angDistance >> 10.000000 --useImed --odir >> Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 >> 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero >> exit status 127 >> >> >> >> >> Any suggestions? >> >> Thank you. >> >> Sincerely, >> Dmitry >> >> >> >> ------------------------------------------------------------------------------ >> Developer Access Program for Intel Xeon Phi Processors >> Access to Intel Xeon Phi processor-based developer platforms. >> With one year of Intel Parallel Studio XE. >> Training and support from Colfax. >> Order your platform today.http://sdm.link/xeonphi >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> > Biocomputing unithttp://biocomp.cnb.csic.es > 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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors Access to > Intel Xeon Phi processor-based developer platforms. With one year > of Intel Parallel Studio XE. Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ scipion-users > mailing list sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es 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 ------------------------------------------------------------------------ |
|
From: Grigory S. <sha...@gm...> - 2016-11-07 15:49:03
|
Hi Dmitry, sorry I didn't look carefully first time. I guess Carlos Oscar can help you with the error with alpha values in significant protocol. I have attached the log files you sent me. [32mxmipp_reconstruct_significant -i Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd --sym d6 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000 --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed --odir Runs/001412_XmippProtReconstructSignificant/tmp/iter001 --alpha0 0.200000 --alphaF 0.200000 --numberOfVolumes 1 [0m Setting iterations to 1 because of --dontReconstruct Input metadata : Runs/001412_XmippProtReconstructSignificant/extra/input_classes.xmd Output directory : Runs/001412_XmippProtReconstructSignificant/tmp/iter001 Initial significance : 0.2 Final significance : 0.2 Number of iterations : 1 Keep intermediate volumes : 0 Angular sampling : 5 Maximum shift : -1 Minimum tilt : 0 Maximum tilt : 90 Use Imed : 1 Angular distance : 10 Apply Fisher : 0 Reconstruct : 0 useForValidation : 0 Symmetry for projections : d6 Number of volumes : 1 [1;31mXMIPP_ERROR 2: Incorrect argument received [0m [1;31m [1;31mAlpha values are too large: reduce the error such that the error times the symmetry number is smaller than 1 [0m [0m [1;31mFile: software/em/xmipp/libraries/reconstruction/reconstruct_significant.cpp line: 737 Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. Institute of Genetics and Molecular and Cellular Biology Integrated Structural Biology Department (CBI) 1, rue Laurent Fries 67404 Illkirch, France tel. 03 69 48 51 00 e-mail: sh...@ig... On Mon, Nov 7, 2016 at 4:30 PM, Carlos Oscar Sorzano <co...@cn...> wrote: > Dear Dmitry, > > as Grigori says, only with these errors it is hard to say what is going > on, is there any other error message? > > Kind regards, Carlos Oscar > > On 11/07/16 13:22, Dmitry Semchonok wrote: > > Dear colleagues, > > I have a problem with running > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>: > > > I faced the following errors: > > xmipp3 - ctf_correct_wiener2d > <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>: > Protocol failed: Command 'srun `which xmipp_mpi_ctf_correct_wiener2d` > -i Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd -o > Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk > --save_metadata_stack Runs/001129_XmippProtCTFCorrec > tWiener2D/corrected_ctf_particles.xmd --pad 2 --wc -1.0 > --sampling_rate 2.24' returned non-zero exit status 127 > > > xmipp3 - reconstruct significant > <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant> > Protocol failed: Command 'srun `which xmipp_mpi_reconstruct_significant` > -i Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd > --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000 > --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed > --odir Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0 > 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit > status 127 > > > > > Any suggestions? > > Thank you. > > Sincerely, > Dmitry > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://biocomp.cnb.csic.es > 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 > ------------------------------------------------------------------------ > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
1 message has been excluded from this view by a project administrator.
