Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. ) However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey
Hi Zoey, What was the "Modeller web service job ID” reported in the log for your Modeller job? --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 27, 2023, at 2:40 PM, Yang, Li-Yen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. )
However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :
From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong?
Thank you! I really appreciate it!
Best, Zoey _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hello Eric, The ID is EOGG2KP8FQQJNC4G, Thank you! Best, Zoey From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Monday, November 27, 2023 at 7:52 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError Hi Zoey, What was the "Modeller web service job ID” reported in the log for your Modeller job? --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 27, 2023, at 2:40 PM, Yang, Li-Yen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. ) However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu<mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email. --Eric Eric Pettersen UCSF Computer Graphics Lab
Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent. --Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Hi Eric, Thank you so much for the response! You are right! I didn’t use the alignment file. I directly uploaded a template structure in pdb and associated a target sequence with it. Can you provide me some guidance on the correct way to do it? I’m guessing if I just associated the target sequence with the structure directly, Chimera would automatically generate an alignment for it before modeling the structure? If so, is this the correct way to do it? I saw a tutorial provided https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html. In the Comparative Modeling Tutorial section, I think the alignment is generated after doing the blast search to find a template structure? But in my case, I already have a pdb structure that I want to use as a template, so I am not doing a blast search to find the template. Is there a way I can obtain the alignment in Chimera in this case? Thank you so much for your help! Best, Zoey From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Tuesday, November 28, 2023 at 2:32 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent. --Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Hi Zoey, As per Eric's explanation: it should generally work like in the tutorial where you can directly associate the template with the target sequence, but in your specific case, that approach did not work because the target sequence had a deletion relative to the template sequence. We now have a bugreport ticket to fix that situation. In the meanwhile, however, you can use the sequence alignment file that Eric provided in a separate email to you (in case that was private data). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2023, at 12:26 PM, Yang, Li-Yen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thank you so much for the response!
You are right! I didn’t use the alignment file. I directly uploaded a template structure in pdb and associated a target sequence with it.
Can you provide me some guidance on the correct way to do it? I’m guessing if I just associated the target sequence with the structure directly, Chimera would automatically generate an alignment for it before modeling the structure? If so, is this the correct way to do it?
I saw a tutorial provided https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html. In the Comparative Modeling Tutorial section, I think the alignment is generated after doing the blast search to find a template structure? But in my case, I already have a pdb structure that I want to use as a template, so I am not doing a blast search to find the template. Is there a way I can obtain the alignment in Chimera in this case?
Thank you so much for your help!
Best, Zoey
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Tuesday, November 28, 2023 at 2:32 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError
Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent.
--Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
P.S. another way you could do it, if Eric hadn't already provided the alignment, is to open the sequence of the target and the structure of the template, then in the sequence window menu choose File... Add Sequence, then in the resulting dialog choose the option to add the sequence from the structure ... then you would have a pairwise sequence alignment. A few different ways to get the needed inputs for Modeller are outlined here: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches> Elaine
On Nov 28, 2023, at 12:52 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Zoey, As per Eric's explanation: it should generally work like in the tutorial where you can directly associate the template with the target sequence, but in your specific case, that approach did not work because the target sequence had a deletion relative to the template sequence.
We now have a bugreport ticket to fix that situation. In the meanwhile, however, you can use the sequence alignment file that Eric provided in a separate email to you (in case that was private data).
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2023, at 12:26 PM, Yang, Li-Yen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thank you so much for the response!
You are right! I didn’t use the alignment file. I directly uploaded a template structure in pdb and associated a target sequence with it.
Can you provide me some guidance on the correct way to do it? I’m guessing if I just associated the target sequence with the structure directly, Chimera would automatically generate an alignment for it before modeling the structure? If so, is this the correct way to do it?
I saw a tutorial provided https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html. In the Comparative Modeling Tutorial section, I think the alignment is generated after doing the blast search to find a template structure? But in my case, I already have a pdb structure that I want to use as a template, so I am not doing a blast search to find the template. Is there a way I can obtain the alignment in Chimera in this case?
Thank you so much for your help!
Best, Zoey
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Tuesday, November 28, 2023 at 2:32 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError
Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent.
--Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Thank you, Elaine and Eric! The problem is solved. From: Elaine Meng <meng@cgl.ucsf.edu> Date: Tuesday, November 28, 2023 at 4:02 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: Chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError P.S. another way you could do it, if Eric hadn't already provided the alignment, is to open the sequence of the target and the structure of the template, then in the sequence window menu choose File... Add Sequence, then in the resulting dialog choose the option to add the sequence from the structure ... then you would have a pairwise sequence alignment. A few different ways to get the needed inputs for Modeller are outlined here: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches> Elaine
On Nov 28, 2023, at 12:52 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Zoey, As per Eric's explanation: it should generally work like in the tutorial where you can directly associate the template with the target sequence, but in your specific case, that approach did not work because the target sequence had a deletion relative to the template sequence.
We now have a bugreport ticket to fix that situation. In the meanwhile, however, you can use the sequence alignment file that Eric provided in a separate email to you (in case that was private data).
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2023, at 12:26 PM, Yang, Li-Yen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thank you so much for the response!
You are right! I didn’t use the alignment file. I directly uploaded a template structure in pdb and associated a target sequence with it.
Can you provide me some guidance on the correct way to do it? I’m guessing if I just associated the target sequence with the structure directly, Chimera would automatically generate an alignment for it before modeling the structure? If so, is this the correct way to do it?
I saw a tutorial provided https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html. In the Comparative Modeling Tutorial section, I think the alignment is generated after doing the blast search to find a template structure? But in my case, I already have a pdb structure that I want to use as a template, so I am not doing a blast search to find the template. Is there a way I can obtain the alignment in Chimera in this case?
Thank you so much for your help!
Best, Zoey
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Tuesday, November 28, 2023 at 2:32 PM To: Yang, Li-Yen <zoeyxyang@gatech.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [chimera] modeller.SequenceMismatchError
Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent.
--Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Eric Pettersen -
Yang, Li-Yen