RR distance map, scale normalization
Hi, I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white. Thanks. Best wishes, Arvind.
Hi Arvind, Unfortunately not, it is a limitation of RR distance maps. It is mentioned in the technical notes section at the bottom of the page, "Coloring is applied across the full value range.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistm...> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2019, at 12:11 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi,
I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white.
Thanks. Best wishes, Arvind.
Dear Chimera, Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? Thanks H.
Hi Hernando, This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can’t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course. Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory. —Eric Eric Pettersen UCSF Computer Graphics Lab
On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera,
Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script?
Thanks
H.
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Dear Chimera, How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info). Thanks Hernando
Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save. —Eric Eric Pettersen UCSF Computer Graphics Lab
On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera,
How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info).
Thanks
Hernando
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Hi Eric, I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script. Here is sample of an association file produced by the Multialign viewer struct1 associates with seq1 chain K 1 - GLU 390.K 2 - ASN 391.K 3 - SER 392.K 4 - GLN 393.K 5 - VAL 394.K .. .. .. struct2 associates with seq2 chain K 1 - ALA 5.K 2 - GLU 6.K 3 - SER 7.K 4 - ASN 8.K 5 - ILE 9.K 6 - LYS 10.K 7 - VAL 11.K 8 - MET 12.K 9 - CYS 13.K 10 - ARG 14.K .. .. .. The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds with S392 in struct1). This is the info I need. Thanks Hernando From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Monday, May 06, 2019 5:39 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save. —Eric Eric Pettersen UCSF Computer Graphics Lab On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>> wrote: Dear Chimera, How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info). Thanks Hernando _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C51110f314a584e1bfc2408d6d26b397a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636927755309838233&sdata=%2BYo2%2BTmWBhps5Z54XBD0UodsOG26SrJ9wEgate2sgJ4%3D&reserved=0>
Ah, in that case if your Multalign Viewer instance is in a variable named ‘mav', call: mav.saveAssocInfo(“save-file-path”) —Eric
On May 7, 2019, at 8:00 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Hi Eric,
I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script.
Here is sample of an association file produced by the Multialign viewer
struct1 associates with seq1 chain K 1 - GLU 390.K 2 - ASN 391.K 3 - SER 392.K 4 - GLN 393.K 5 - VAL 394.K .. .. .. struct2 associates with seq2 chain K 1 - ALA 5.K 2 - GLU 6.K 3 - SER 7.K 4 - ASN 8.K 5 - ILE 9.K 6 - LYS 10.K 7 - VAL 11.K 8 - MET 12.K 9 - CYS 13.K 10 - ARG 14.K .. .. ..
The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds with S392 in struct1). This is the info I need.
Thanks
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Monday, May 06, 2019 5:39 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info
Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Dear Chimera,
How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info).
Thanks
Hernando
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That will work. So the question now is how to assign the Multialign Viewer to a variable when opening a file with pre-aligned sequences. Eg after running the following command runCommand('open myseqalignment.fas') the multialign window opens and the sequence-structure associations are made. How can I access this Multialign viewer instance? Is there something equivalent to mav = the_multialign_viewer_created_when_opening_a_file Thanks again Hernando From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, May 07, 2019 1:04 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info Ah, in that case if your Multalign Viewer instance is in a variable named ‘mav', call: mav.saveAssocInfo(“save-file-path”) —Eric On May 7, 2019, at 8:00 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>> wrote: Hi Eric, I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script. Here is sample of an association file produced by the Multialign viewer struct1 associates with seq1 chain K 1 - GLU 390.K 2 - ASN 391.K 3 - SER 392.K 4 - GLN 393.K 5 - VAL 394.K .. .. .. struct2 associates with seq2 chain K 1 - ALA 5.K 2 - GLU 6.K 3 - SER 7.K 4 - ASN 8.K 5 - ILE 9.K 6 - LYS 10.K 7 - VAL 11.K 8 - MET 12.K 9 - CYS 13.K 10 - ARG 14.K .. .. .. The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds with S392 in struct1). This is the info I need. Thanks Hernando From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Monday, May 06, 2019 5:39 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save. —Eric Eric Pettersen UCSF Computer Graphics Lab On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>> wrote: Dear Chimera, How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info). Thanks Hernando _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C392c01418f1f4e7ee7c908d6d30df5a1%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636928454257389732&sdata=fsdlVvyzLi0eO49FgZ0aafUGjYEVaoJxx2mIrHu%2Bdsc%3D&reserved=0> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C392c01418f1f4e7ee7c908d6d30df5a1%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636928454257399722&sdata=aBGcPm2KniPJ1VszhisxZpz61hCBTZERueKpqrShkbo%3D&reserved=0>
See this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html> —Eric
On May 7, 2019, at 10:45 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
That will work. So the question now is how to assign the Multialign Viewer to a variable when opening a file with pre-aligned sequences. Eg after running the following command
runCommand('open myseqalignment.fas')
the multialign window opens and the sequence-structure associations are made. How can I access this Multialign viewer instance? Is there something equivalent to
mav = the_multialign_viewer_created_when_opening_a_file
Thanks again
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, May 07, 2019 1:04 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info
Ah, in that case if your Multalign Viewer instance is in a variable named ‘mav', call:
mav.saveAssocInfo(“save-file-path”)
—Eric
On May 7, 2019, at 8:00 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Hi Eric,
I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script.
Here is sample of an association file produced by the Multialign viewer
struct1 associates with seq1 chain K 1 - GLU 390.K 2 - ASN 391.K 3 - SER 392.K 4 - GLN 393.K 5 - VAL 394.K .. .. .. struct2 associates with seq2 chain K 1 - ALA 5.K 2 - GLU 6.K 3 - SER 7.K 4 - ASN 8.K 5 - ILE 9.K 6 - LYS 10.K 7 - VAL 11.K 8 - MET 12.K 9 - CYS 13.K 10 - ARG 14.K .. .. ..
The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds with S392 in struct1). This is the info I need.
Thanks
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>] Sent: Monday, May 06, 2019 5:39 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info
Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Dear Chimera,
How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info).
Thanks
Hernando
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Thanks for your reply Elaine. Have a nice weekend Arvind. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, May 3, 2019 4:19:39 PM To: Arvind SHARMA Cc: Chimera User Help Subject: Re: [Chimera-users] RR distance map, scale normalization Hi Arvind, Unfortunately not, it is a limitation of RR distance maps. It is mentioned in the technical notes section at the bottom of the page, "Coloring is applied across the full value range.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistm...> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2019, at 12:11 AM, Arvind SHARMA <arvind.sharma@pasteur.fr> wrote:
Hi,
I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white.
Thanks. Best wishes, Arvind.
participants (4)
-
Arvind SHARMA -
Elaine Meng -
Eric Pettersen -
Hernando J Sosa