Help using Chimera with SFLD - I cannot 'view in chimera'
Dear Elaine, or other Chimera Guru, I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2 Anne-Frances Miller Professor of Chemistry University of Kentucky
Dear Anne-Frances, I believe something has gone awry with SFLD outputs, at least those relating to Chimera: (A) exactly as you reported, I cannot get the stockholm-format alignment file referenced in the chimerax (chimera web data) file. The URL for the sto file gives an error in the browser, e.g. [Errno 13] Permission denied: u'/tmp/sfld/alignment_WSLmTdwA.sto’ and the local temp-data file given in the Chimera error message does not exist, as far as I can tell. In my tests, Chimera does not crash, it just gives that error message that the stockholm file is no good. (B) I cannot test the active-site sessions because when I view any family in the SFLD that I know should have such a session, it does not show the active-site image in the page like it used to. (normally I would click that image to get the session for Chimera) I’m not sure who may be on the hook to try to resolve these problems, but I’ll make some enquiries and will report back if any progress is made. Sorry about these problems, and thanks for reporting them! At least you know it isn’t something you did wrong. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 11, 2017, at 5:53 AM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Dear Elaine, or other Chimera Guru,
I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2
Anne-Frances Miller Professor of Chemistry University of Kentucky
I’ve also reproduced the crashing behavior, but I’m pretty sure it is due to the SFLD output problem rather than Chimera per se. For the developers’ benefit: I got the crash by viewing an alignment in the SFLD viewer, and in the resulting page with the alignment, clicking the small Chimera icon to open MSF format in Chimera. If I instead click the text next to it “Open raw MSA file” the browser then shows “Internal Server Error” suggesting it is again a failure to serve up the proper data. However, downloading data as fasta (unaligned, so not what you wanted) and downloading networks seems to work OK. Elaine
On Nov 13, 2017, at 10:26 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Anne-Frances, I believe something has gone awry with SFLD outputs, at least those relating to Chimera:
(A) exactly as you reported, I cannot get the stockholm-format alignment file referenced in the chimerax (chimera web data) file. The URL for the sto file gives an error in the browser, e.g. [Errno 13] Permission denied: u'/tmp/sfld/alignment_WSLmTdwA.sto’ and the local temp-data file given in the Chimera error message does not exist, as far as I can tell.
In my tests, Chimera does not crash, it just gives that error message that the stockholm file is no good.
(B) I cannot test the active-site sessions because when I view any family in the SFLD that I know should have such a session, it does not show the active-site image in the page like it used to. (normally I would click that image to get the session for Chimera)
I’m not sure who may be on the hook to try to resolve these problems, but I’ll make some enquiries and will report back if any progress is made. Sorry about these problems, and thanks for reporting them! At least you know it isn’t something you did wrong. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 11, 2017, at 5:53 AM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Dear Elaine, or other Chimera Guru,
I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2
Anne-Frances Miller Professor of Chemistry University of Kentucky
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Anne-Frances et al., One piece of this has been fixed: now in the View Alignment tab you can choose to use Chimera as the viewer and it will work (via download of chimerax file that refers to a a URL with a Stockholm sequence alignment file). Also working: choosing SFLD viewer for the sequence alignment and then on the resulting page, clicking the small Chimera icon to view it in Chimera. If you know the PDB ID(s) for corresponding structures, you can open them directly (not via SFLD) in Chimera at the same time as the alignment, with automatic association for crosstalk with the alignment. However, at the SFLD website, clicking the text “open raw MSA file” still gives an error, and I still don’t see “active site” images/sessions. I hope this helps, Elaine
On Nov 13, 2017, at 10:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I’ve also reproduced the crashing behavior, but I’m pretty sure it is due to the SFLD output problem rather than Chimera per se.
For the developers’ benefit: I got the crash by viewing an alignment in the SFLD viewer, and in the resulting page with the alignment, clicking the small Chimera icon to open MSF format in Chimera. If I instead click the text next to it “Open raw MSA file” the browser then shows “Internal Server Error” suggesting it is again a failure to serve up the proper data.
However, downloading data as fasta (unaligned, so not what you wanted) and downloading networks seems to work OK.
Elaine
On Nov 13, 2017, at 10:26 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Anne-Frances, I believe something has gone awry with SFLD outputs, at least those relating to Chimera:
(A) exactly as you reported, I cannot get the stockholm-format alignment file referenced in the chimerax (chimera web data) file. The URL for the sto file gives an error in the browser, e.g. [Errno 13] Permission denied: u'/tmp/sfld/alignment_WSLmTdwA.sto’ and the local temp-data file given in the Chimera error message does not exist, as far as I can tell.
In my tests, Chimera does not crash, it just gives that error message that the stockholm file is no good.
(B) I cannot test the active-site sessions because when I view any family in the SFLD that I know should have such a session, it does not show the active-site image in the page like it used to. (normally I would click that image to get the session for Chimera)
I’m not sure who may be on the hook to try to resolve these problems, but I’ll make some enquiries and will report back if any progress is made. Sorry about these problems, and thanks for reporting them! At least you know it isn’t something you did wrong. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 11, 2017, at 5:53 AM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Dear Elaine, or other Chimera Guru,
I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2
Anne-Frances Miller Professor of Chemistry University of Kentucky
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Anne-Frances et al., I’m happy to report that now the family active site images are back on the SFLD and can be clicked to open the corresponding session in Chimera (it actually downloads a chimerax file with URL reference to the session file, similar to the stockholm-format MSA file). On one of my computers (but not the other!) downloading the chimerax file doesn’t start Chimera, but if I doubleclick the chimerax file icon it does, or I can just open the chimerax file from an already running instance of Chimera. The problem may be with my own personal setup since I have Firefox sharing settings between computers, but happened to name my multiple copies of Chimera differently on the two computers. I hope this helps, Elaine
On Nov 13, 2017, at 3:23 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Anne-Frances et al.,
One piece of this has been fixed: now in the View Alignment tab you can choose to use Chimera as the viewer and it will work (via download of chimerax file that refers to a a URL with a Stockholm sequence alignment file). Also working: choosing SFLD viewer for the sequence alignment and then on the resulting page, clicking the small Chimera icon to view it in Chimera.
If you know the PDB ID(s) for corresponding structures, you can open them directly (not via SFLD) in Chimera at the same time as the alignment, with automatic association for crosstalk with the alignment.
However, at the SFLD website, clicking the text “open raw MSA file” still gives an error, and I still don’t see “active site” images/sessions.
I hope this helps, Elaine
On Nov 13, 2017, at 10:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I’ve also reproduced the crashing behavior, but I’m pretty sure it is due to the SFLD output problem rather than Chimera per se.
For the developers’ benefit: I got the crash by viewing an alignment in the SFLD viewer, and in the resulting page with the alignment, clicking the small Chimera icon to open MSF format in Chimera. If I instead click the text next to it “Open raw MSA file” the browser then shows “Internal Server Error” suggesting it is again a failure to serve up the proper data.
However, downloading data as fasta (unaligned, so not what you wanted) and downloading networks seems to work OK.
Elaine
On Nov 13, 2017, at 10:26 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Anne-Frances, I believe something has gone awry with SFLD outputs, at least those relating to Chimera:
(A) exactly as you reported, I cannot get the stockholm-format alignment file referenced in the chimerax (chimera web data) file. The URL for the sto file gives an error in the browser, e.g. [Errno 13] Permission denied: u'/tmp/sfld/alignment_WSLmTdwA.sto’ and the local temp-data file given in the Chimera error message does not exist, as far as I can tell.
In my tests, Chimera does not crash, it just gives that error message that the stockholm file is no good.
(B) I cannot test the active-site sessions because when I view any family in the SFLD that I know should have such a session, it does not show the active-site image in the page like it used to. (normally I would click that image to get the session for Chimera)
I’m not sure who may be on the hook to try to resolve these problems, but I’ll make some enquiries and will report back if any progress is made. Sorry about these problems, and thanks for reporting them! At least you know it isn’t something you did wrong. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 11, 2017, at 5:53 AM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Dear Elaine, or other Chimera Guru,
I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2
Anne-Frances Miller Professor of Chemistry University of Kentucky
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ SFLD-users mailing list SFLD-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/sfld-users
Thank you very much Elaine, At least I do not feel stupid, but I am sorry that things are not working because it is clear that the SFLD resources are very very powerful. I had done exactly what you suggested: downloaded the large FASTA files, which I then uploaded to Clustal omega. This will not give me the benefit of the HMM that was developed specifically for this data set, but it will be very good nonetheless. Best Wishes and thanks again, Anne-Frances Miller Professor of Chemistry University of Kentucky
On 13Nov 2017, at 7:26 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Anne-Frances, I believe something has gone awry with SFLD outputs, at least those relating to Chimera:
(A) exactly as you reported, I cannot get the stockholm-format alignment file referenced in the chimerax (chimera web data) file. The URL for the sto file gives an error in the browser, e.g. [Errno 13] Permission denied: u'/tmp/sfld/alignment_WSLmTdwA.sto’ and the local temp-data file given in the Chimera error message does not exist, as far as I can tell.
In my tests, Chimera does not crash, it just gives that error message that the stockholm file is no good.
(B) I cannot test the active-site sessions because when I view any family in the SFLD that I know should have such a session, it does not show the active-site image in the page like it used to. (normally I would click that image to get the session for Chimera)
I’m not sure who may be on the hook to try to resolve these problems, but I’ll make some enquiries and will report back if any progress is made. Sorry about these problems, and thanks for reporting them! At least you know it isn’t something you did wrong. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 11, 2017, at 5:53 AM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Dear Elaine, or other Chimera Guru,
I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2
Anne-Frances Miller Professor of Chemistry University of Kentucky
participants (2)
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Anne-Frances Miller -
Elaine Meng