where is "Save each fit when doing multiple alignments" button
Dear all,I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it?Best regard,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 5, 2015, at 7:33 AM, sunyeping <sunyeping@aliyun.com> wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
P.S. I see that NCMI has newer Segger documentation at <https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide> I'll add this link to the Chimera documentation. Elaine On Apr 5, 2015, at 10:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2015, at 7:33 AM, sunyeping <sunyeping@aliyun.com> wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
Dear Elaine, I have read the link provide. However the "Fitting Options" section and the last paragraph of "Fittint models to segments" tutorial still tells us to "check the button to the left of Save each fit when doing multiple alignments". I cannot find this botton and so cannot follow this tutorial. Could you just tell me in this GroEL example how to align the structure to multiple regions and get the last figure of this tutorial?Best regards, Yeping Sun Institute of Microbiology, Chinese Academy of Sciencesalign ------------------------------------------------------------------From:Elaine Meng <meng@cgl.ucsf.edu>Send Time:2015年4月7日(星期二) 07:19To:孙业平 <sunyeping@aliyun.com>Cc:Mailing List <chimera-users@cgl.ucsf.edu>Subject:Re: [Chimera-users] where is "Save each fit when doing multiple alignments" button P.S. I see that NCMI has newer Segger documentation at <https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide> I'll add this link to the Chimera documentation. Elaine On Apr 5, 2015, at 10:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2015, at 7:33 AM, sunyeping <sunyeping@aliyun.com> wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
Dear Yeping Sun, We did not write this tutorial, and I am not aware of any such option. As I said before, I thought it would save each fit anyway (without this option) so my guess is you could ignore that sentence and continue to get the results. But that is a guess. We cannot thoroughly explain tutorials that we didn't write! Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2015, at 6:51 AM, "sunyeping" <sunyeping@aliyun.com> wrote:
Dear Elaine,
I have read the link provide. However the "Fitting Options" section and the last paragraph of "Fittint models to segments" tutorial still tells us to "check the button to the left of Save each fit when doing multiple alignments". I cannot find this botton and so cannot follow this tutorial. Could you just tell me in this GroEL example how to align the structure to multiple regions and get the last figure of this tutorial?
Best regards,
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciencesalign
------------------------------------------------------------------ From:Elaine Meng <meng@cgl.ucsf.edu> Send Time:2015年4月7日(星期二) 07:19 To:孙业平 <sunyeping@aliyun.com> Cc:Mailing List <chimera-users@cgl.ucsf.edu> Subject:Re: [Chimera-users] where is "Save each fit when doing multiple alignments" button
P.S. I see that NCMI has newer Segger documentation at
<https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide>
I'll add this link to the Chimera documentation. Elaine
On Apr 5, 2015, at 10:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2015, at 7:33 AM, sunyeping <sunyeping@aliyun.com> wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi all, That sentence was applicable to an older version of the UI... In the new UI, the equivalent option is “Add top ____ fit(s) to list (empty to add all fits to list)”, and the sentence should be to make that box empty. I’ve just updated the tutorial at the link below with this: https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-gui... <https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide/fitting-a-structure-to-segments> Greg
On Apr 7, 2015, at 11:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yeping Sun, We did not write this tutorial, and I am not aware of any such option. As I said before, I thought it would save each fit anyway (without this option) so my guess is you could ignore that sentence and continue to get the results. But that is a guess. We cannot thoroughly explain tutorials that we didn't write! Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2015, at 6:51 AM, "sunyeping" <sunyeping@aliyun.com> wrote:
Dear Elaine,
I have read the link provide. However the "Fitting Options" section and the last paragraph of "Fittint models to segments" tutorial still tells us to "check the button to the left of Save each fit when doing multiple alignments". I cannot find this botton and so cannot follow this tutorial. Could you just tell me in this GroEL example how to align the structure to multiple regions and get the last figure of this tutorial?
Best regards,
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciencesalign
------------------------------------------------------------------ From:Elaine Meng <meng@cgl.ucsf.edu> Send Time:2015年4月7日(星期二) 07:19 To:孙业平 <sunyeping@aliyun.com> Cc:Mailing List <chimera-users@cgl.ucsf.edu> Subject:Re: [Chimera-users] where is "Save each fit when doing multiple alignments" button
P.S. I see that NCMI has newer Segger documentation at
<https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide>
I'll add this link to the Chimera documentation. Elaine
On Apr 5, 2015, at 10:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2015, at 7:33 AM, sunyeping <sunyeping@aliyun.com> wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Yeping, As Elaine says the tutorial http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting <http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting> is out of date. But it is easy to place copies of the molecule to get the last image in the tutorial. Just fit each selected region (you can select them all by ctrl-clicking one, then press the up arrow key). Then select all the lines in the fit list and use menu entry Fit / Place Molecule Copies. It might help you to read the Chimera documentation on the Fit to Segments tool which describes menu entry Place Molecule Copies. http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/segger/fits... Tom
On Apr 7, 2015, at 6:51 AM, sunyeping wrote:
Dear Elaine,
I have read the link provide. However the "Fitting Options" section and the last paragraph of "Fittint models to segments" tutorial still tells us to "check the button to the left of Save each fit when doing multiple alignments". I cannot find this botton and so cannot follow this tutorial. Could you just tell me in this GroEL example how to align the structure to multiple regions and get the last figure of this tutorial?
Best regards,
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciencesalign
------------------------------------------------------------------ From:Elaine Meng Send Time:2015年4月7日(星期二) 07:19 To:孙业平 Cc:Mailing List <chimera-users@cgl.ucsf.edu> Subject:Re: [Chimera-users] where is "Save each fit when doing multiple alignments" button
P.S. I see that NCMI has newer Segger documentation at
<https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide>
I'll add this link to the Chimera documentation. Elaine
On Apr 5, 2015, at 10:34 AM, Elaine Meng wrote:
Dear Yepin Sun, I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2015, at 7:33 AM, sunyeping wrote:
Dear all, I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it? Best regard, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Greg Pintilie -
sunyeping -
Tom Goddard