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Crosslinks not displaying properly #79

Closed KatGS92 closed 3 years ago

KatGS92 commented 3 years ago

image

colin-combe commented 3 years ago

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. (colin.combe@ed.ac.uk) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

colin-combe commented 3 years ago

(sorted out)

KatGS92 commented 3 years ago

Hi Colin,

I’ve been trying to analyse some xlink data using XiVIEW (in particular the export pseudobonds, circular plot and 3D view functions are very useful) but am having a couple of issues. So, the crosslinked residues display correctly in the match table (i.e. all should be either K-K or K-N-terminus bonds) but when I use the 3D view or circular plots they are showing as links to different redisues (see attached screen shots). Is there something in my data that is causing this? I’ve attached my csv file for reference. Are you able to help me in any way?

Kind regards, Kat

                                                              ***@***.***D7459F.3661E1A0] ***@***.***D7459E.7EEF4BC0]

From: Colin @.> Sent: Thursday, April 29, 2021 7:52 AM To: Rappsilber-Laboratory/xiView_container @.> Cc: Stevens, K.G. (Katherine) @.>; Author @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. @.**@.>) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-828957728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFESEHXJTWNYYP4C3LTTLDXWNANCNFSM43X7CR5Q.

colin-combe commented 3 years ago

Hi, I'm away from my desk at moment and cant check your csv file.

Could it be that the search sequences aren't ths same as the canonical uniprot sequences but they're getting replaced with the uniprot one?

If this is the case u should be able to correct it by uploading a fasta file with the search sequences alongside the csv.

C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.> Sent: Monday, May 10, 2021 12:20:46 PM To: Rappsilber-Laboratory/xiView_container @.> Cc: COMBE Colin @.>; State change @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

I’ve been trying to analyse some xlink data using XiVIEW (in particular the export pseudobonds, circular plot and 3D view functions are very useful) but am having a couple of issues. So, the crosslinked residues display correctly in the match table (i.e. all should be either K-K or K-N-terminus bonds) but when I use the 3D view or circular plots they are showing as links to different redisues (see attached screen shots). Is there something in my data that is causing this? I’ve attached my csv file for reference. Are you able to help me in any way?

Kind regards, Kat

@.D7459F.3661E1A0] @.D7459E.7EEF4BC0]

From: Colin @.> Sent: Thursday, April 29, 2021 7:52 AM To: Rappsilber-Laboratory/xiView_container @.> Cc: Stevens, K.G. (Katherine) @.>; Author @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. @.**@.>) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-828957728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFESEHXJTWNYYP4C3LTTLDXWNANCNFSM43X7CR5Q.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836573343, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAHOVR4WFH4ULEBP7UVSXLLTM66Q5ANCNFSM43X7CR5Q.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

KatGS92 commented 3 years ago

Hi Colin,

Thanks for getting back to me. The Uniprot acc. #s in the search database fasta were obtained directly from Uniprot. The linked residues in the csv correspond to the correct residues in the uniprot sequence, so I don’t think this is the issue. The links are also correctly assigned to lysine residues in the XiVIEW match table, just not in the circular view or 3d views, so unless these plots are somehow generated using different sequences I don’t know how this is possible.

Thanks, Katherine

From: Colin @.> Sent: Monday, May 10, 2021 6:30 PM To: Rappsilber-Laboratory/xiView_container @.> Cc: Stevens, K.G. (Katherine) @.>; Author @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

Hi, I'm away from my desk at moment and cant check your csv file.

Could it be that the search sequences aren't ths same as the canonical uniprot sequences but they're getting replaced with the uniprot one?

If this is the case u should be able to correct it by uploading a fasta file with the search sequences alongside the csv.

C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.<mailto:@.>> Sent: Monday, May 10, 2021 12:20:46 PM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: COMBE Colin @.<mailto:@.>>; State change @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

I’ve been trying to analyse some xlink data using XiVIEW (in particular the export pseudobonds, circular plot and 3D view functions are very useful) but am having a couple of issues. So, the crosslinked residues display correctly in the match table (i.e. all should be either K-K or K-N-terminus bonds) but when I use the 3D view or circular plots they are showing as links to different redisues (see attached screen shots). Is there something in my data that is causing this? I’ve attached my csv file for reference. Are you able to help me in any way?

Kind regards, Kat

@.D7459F.3661E1A0<mailto:@.D7459F.3661E1A0>] @.D7459E.7EEF4BC0<mailto:@.D7459E.7EEF4BC0>]

From: Colin @.<mailto:@.>> Sent: Thursday, April 29, 2021 7:52 AM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: Stevens, K.G. (Katherine) @.<mailto:@.>>; Author @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. @.**@.mailto:***@***.******@***.***>) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-828957728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFESEHXJTWNYYP4C3LTTLDXWNANCNFSM43X7CR5Q.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836573343, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAHOVR4WFH4ULEBP7UVSXLLTM66Q5ANCNFSM43X7CR5Q.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836926016, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFGDIYCU3QZS34VRUGTTNACZHANCNFSM43X7CR5Q.

colin-combe commented 3 years ago

Ok, that doesn't sound right. I wont be able to have a proper look at what's happening until thursday. I'll get back to you then, Cheers, C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.> Sent: Tuesday, May 11, 2021 7:58:48 AM To: Rappsilber-Laboratory/xiView_container @.> Cc: COMBE Colin @.>; State change @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

Thanks for getting back to me. The Uniprot acc. #s in the search database fasta were obtained directly from Uniprot. The linked residues in the csv correspond to the correct residues in the uniprot sequence, so I don’t think this is the issue. The links are also correctly assigned to lysine residues in the XiVIEW match table, just not in the circular view or 3d views, so unless these plots are somehow generated using different sequences I don’t know how this is possible.

Thanks, Katherine

From: Colin @.> Sent: Monday, May 10, 2021 6:30 PM To: Rappsilber-Laboratory/xiView_container @.> Cc: Stevens, K.G. (Katherine) @.>; Author @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

Hi, I'm away from my desk at moment and cant check your csv file.

Could it be that the search sequences aren't ths same as the canonical uniprot sequences but they're getting replaced with the uniprot one?

If this is the case u should be able to correct it by uploading a fasta file with the search sequences alongside the csv.

C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.<mailto:@.>> Sent: Monday, May 10, 2021 12:20:46 PM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: COMBE Colin @.<mailto:@.>>; State change @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

I’ve been trying to analyse some xlink data using XiVIEW (in particular the export pseudobonds, circular plot and 3D view functions are very useful) but am having a couple of issues. So, the crosslinked residues display correctly in the match table (i.e. all should be either K-K or K-N-terminus bonds) but when I use the 3D view or circular plots they are showing as links to different redisues (see attached screen shots). Is there something in my data that is causing this? I’ve attached my csv file for reference. Are you able to help me in any way?

Kind regards, Kat

@.D7459F.3661E1A0<mailto:@.D7459F.3661E1A0>] @.D7459E.7EEF4BC0<mailto:@.D7459E.7EEF4BC0>]

From: Colin @.<mailto:@.>> Sent: Thursday, April 29, 2021 7:52 AM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: Stevens, K.G. (Katherine) @.<mailto:@.>>; Author @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. @.**@.mailto:***@***.******@***.***>) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-828957728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFESEHXJTWNYYP4C3LTTLDXWNANCNFSM43X7CR5Q.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836573343, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAHOVR4WFH4ULEBP7UVSXLLTM66Q5ANCNFSM43X7CR5Q.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836926016, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFGDIYCU3QZS34VRUGTTNACZHANCNFSM43X7CR5Q.

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KatGS92 commented 3 years ago

Great, thank you!

From: Colin @.> Sent: Tuesday, May 11, 2021 9:26 AM To: Rappsilber-Laboratory/xiView_container @.> Cc: Stevens, K.G. (Katherine) @.>; Author @.> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

Ok, that doesn't sound right. I wont be able to have a proper look at what's happening until thursday. I'll get back to you then, Cheers, C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.<mailto:@.>> Sent: Tuesday, May 11, 2021 7:58:48 AM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: COMBE Colin @.<mailto:@.>>; State change @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

Thanks for getting back to me. The Uniprot acc. #s in the search database fasta were obtained directly from Uniprot. The linked residues in the csv correspond to the correct residues in the uniprot sequence, so I don’t think this is the issue. The links are also correctly assigned to lysine residues in the XiVIEW match table, just not in the circular view or 3d views, so unless these plots are somehow generated using different sequences I don’t know how this is possible.

Thanks, Katherine

From: Colin @.<mailto:@.>> Sent: Monday, May 10, 2021 6:30 PM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.>> Cc: Stevens, K.G. (Katherine) @.<mailto:@.>>; Author @.<mailto:@.>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

Hi, I'm away from my desk at moment and cant check your csv file.

Could it be that the search sequences aren't ths same as the canonical uniprot sequences but they're getting replaced with the uniprot one?

If this is the case u should be able to correct it by uploading a fasta file with the search sequences alongside the csv.

C

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: KatSUtrecht @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Sent: Monday, May 10, 2021 12:20:46 PM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Cc: COMBE Colin @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; State change @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi Colin,

I’ve been trying to analyse some xlink data using XiVIEW (in particular the export pseudobonds, circular plot and 3D view functions are very useful) but am having a couple of issues. So, the crosslinked residues display correctly in the match table (i.e. all should be either K-K or K-N-terminus bonds) but when I use the 3D view or circular plots they are showing as links to different redisues (see attached screen shots). Is there something in my data that is causing this? I’ve attached my csv file for reference. Are you able to help me in any way?

Kind regards, Kat

@.D7459F.3661E1A0<mailto:@.D7459F.3661E1A0mailto:***@***.***D7459F.3661E1A0%3cmailto:***@***.***D7459F.3661E1A0>] @.D7459E.7EEF4BC0<mailto:@.D7459E.7EEF4BC0mailto:***@***.***D7459E.7EEF4BC0%3cmailto:***@***.***D7459E.7EEF4BC0>]

From: Colin @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Sent: Thursday, April 29, 2021 7:52 AM To: Rappsilber-Laboratory/xiView_container @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Cc: Stevens, K.G. (Katherine) @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Author @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Subject: Re: [Rappsilber-Laboratory/xiView_container] Crosslinks not displaying properly (#79)

yes - I can confirm that these crosslinks are not displaying properly

I would need to know more about how it happened to fix it. Is this from a file you uploaded to crosslinkviewer.org? If so, you could email me the link to the page and I'll test it. @.**@.mailto:***@***.******@***.***<mailto:***@***.******@***.***%3cmailto:***@***.******@***.***>>) You can also post the link here, though that means everyone can see your data.

Other info that might help - what browser were you using? does it fix itself if you change the protein to a circle and then back to a bar? Do you know if you did something specific to make it happen? Is it always links to that same protein that are broken?

cheers, Colin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-828957728, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFESEHXJTWNYYP4C3LTTLDXWNANCNFSM43X7CR5Q.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836573343, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAHOVR4WFH4ULEBP7UVSXLLTM66Q5ANCNFSM43X7CR5Q.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Rappsilber-Laboratory/xiView_container/issues/79#issuecomment-836926016, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AT4DXFGDIYCU3QZS34VRUGTTNACZHANCNFSM43X7CR5Q.

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colin-combe commented 3 years ago

(@KatSUtrecht - I emailed u yesterday to say I can't access the csv file to test it)