您好： 我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。 张晓飞 202521100284@stu.ujn.edu.cn
Here's Google's English translation of this inquiry: Dear Support Team, Hello. On September 14, 2026, I submitted Job L7VGGZ7PMNMYBWAR via the web service of ChimeraX 1.12. The task was a Modeller refinement to fill in the internal missing loops for the 9IM3 dodecamer (12 chains, ~4,800 residues). The job status returned as "failed". The stderr is empty, and the stdout cuts off midway through the bond angle violations list, with no models summary provided. While IL00010001.pdb and B99990001.pdb were generated, DL00010001.pdb is missing. In B99990001.pdb, all 12 chains are present with no missing residues; however, the residue numbering runs continuously from 1 to 6564 rather than being partitioned by individual chains. I suspect the job was forcefully terminated due to the computation time exceeding the server's single-task limit. Could you please clarify the following: Is there a maximum time limit per job for this service? For multi-chain tasks of this scale, do you recommend submitting them chain by chain? Can B99990001.pdb be reliably used as the final structure with the loops completed? I look forward to hearing from you. Thank you very much for your time and assistance. Best regards,
On Sep 17, 2026, at 1:25 AM, 张晓飞 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
您好： 我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。
Eric is the modeller expert and better suited to answer questions 2 and 3, but I can say that the maximum time limit per job is 6 hours. — Zach
On 17 Sep 2026, at 16:42, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Here's Google's English translation of this inquiry:
Dear Support Team,
Hello. On September 14, 2026, I submitted Job L7VGGZ7PMNMYBWAR via the web service of ChimeraX 1.12. The task was a Modeller refinement to fill in the internal missing loops for the 9IM3 dodecamer (12 chains, ~4,800 residues). The job status returned as "failed". The stderr is empty, and the stdout cuts off midway through the bond angle violations list, with no models summary provided. While IL00010001.pdb and B99990001.pdb were generated, DL00010001.pdb is missing. In B99990001.pdb, all 12 chains are present with no missing residues; however, the residue numbering runs continuously from 1 to 6564 rather than being partitioned by individual chains.
I suspect the job was forcefully terminated due to the computation time exceeding the server's single-task limit. Could you please clarify the following: 1. Is there a maximum time limit per job for this service? 2. For multi-chain tasks of this scale, do you recommend submitting them chain by chain? 3. Can B99990001.pdb be reliably used as the final structure with the loops completed? I look forward to hearing from you. Thank you very much for your time and assistance. Best regards,
On Sep 17, 2026, at 1:25 AM, 张晓飞 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
您好： 我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi All, When I model missing loops in a homomultimer using Modeler, I always model just one monomer and then make copies and align them with the original monomers. Best regards Sasha Sent from my Galaxy -------- Original message --------From: Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: 18/09/2026 02:45 (GMT+02:00) To: 张晓飞 <zhangxf@stu.ujn.edu.cn> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: (no subject) Here's Google's English translation of this inquiry:Dear Support Team,Hello. On September 14, 2026, I submitted Job L7VGGZ7PMNMYBWAR via the web service of ChimeraX 1.12. The task was a Modeller refinement to fill in the internal missing loops for the 9IM3 dodecamer (12 chains, ~4,800 residues).The job status returned as "failed". The stderr is empty, and the stdout cuts off midway through the bond angle violations list, with no models summary provided. While IL00010001.pdb and B99990001.pdb were generated, DL00010001.pdb is missing. In B99990001.pdb, all 12 chains are present with no missing residues; however, the residue numbering runs continuously from 1 to 6564 rather than being partitioned by individual chains.I suspect the job was forcefully terminated due to the computation time exceeding the server's single-task limit. Could you please clarify the following:Is there a maximum time limit per job for this service?For multi-chain tasks of this scale, do you recommend submitting them chain by chain?Can B99990001.pdb be reliably used as the final structure with the loops completed?I look forward to hearing from you. Thank you very much for your time and assistance.Best regards,On Sep 17, 2026, at 1:25 AM, 张晓飞 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:您好：我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。
I think Sasha's advice is spot on here. If I try to generate just one model for the missing loops of the entire dodecamer, the job fails after running more than 5 hours because the maximum number of retries to get a status update is exceeded. The general procedure for what Sasha is suggesting would be: 1) Get a sequence viewer with only one of the chains associated. If you have a viewer with many chains associated, use that viewer's "Structure→Associations..." context menu item to reduce the associations to just one chain. Alternatively, you can open a viewer for just chain A with the "seq chain /A" command. 2) Use Modeller normally to generate a model for that chain with the loops filled in. 3) Generate 11 more copies of the filled chain with "combine" commands. 4) Use MatchMaker to align the copies onto the dodecamer chains. 5) Use the "combine" command again to combine the separate chain models into a single model. 6) If you don't like the chain ID assignments for the combined model, use the "Tools→Structure Editing→Change Chain IDs" tool to change them. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 17, 2026, at 10:56 PM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, When I model missing loops in a homomultimer using Modeler, I always model just one monomer and then make copies and align them with the original monomers. Best regards Sasha
Sent from my Galaxy
-------- Original message -------- From: Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: 18/09/2026 02:45 (GMT+02:00) To: 张晓飞 <zhangxf@stu.ujn.edu.cn> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: (no subject)
Here's Google's English translation of this inquiry:
Dear Support Team,
Hello. On September 14, 2026, I submitted Job L7VGGZ7PMNMYBWAR via the web service of ChimeraX 1.12. The task was a Modeller refinement to fill in the internal missing loops for the 9IM3 dodecamer (12 chains, ~4,800 residues). The job status returned as "failed". The stderr is empty, and the stdout cuts off midway through the bond angle violations list, with no models summary provided. While IL00010001.pdb and B99990001.pdb were generated, DL00010001.pdb is missing. In B99990001.pdb, all 12 chains are present with no missing residues; however, the residue numbering runs continuously from 1 to 6564 rather than being partitioned by individual chains.
I suspect the job was forcefully terminated due to the computation time exceeding the server's single-task limit. Could you please clarify the following: Is there a maximum time limit per job for this service? For multi-chain tasks of this scale, do you recommend submitting them chain by chain? Can B99990001.pdb be reliably used as the final structure with the loops completed? I look forward to hearing from you. Thank you very much for your time and assistance. Best regards,
On Sep 17, 2026, at 1:25 AM, 张晓飞 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
您好： 我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Eric, Thank you very much for the detailed explanation and the step-by-step procedure — this is exactly what I need. I will follow the workflow: model only chain A with Modeller, then use "combine" and MatchMaker to build the full dodecamer. Thanks also to Sasha for the practical suggestion, and to Zach and Tom for the earlier explanations. I really appreciate how responsive and helpful the ChimeraX team and community are. Best regards, Xiaofei 张晓飞 202521100284@stu.ujn.edu.cn Original: From：Eric Pettersen <pett@cgl.ucsf.edu>Date：2026-09-19 07:59:48(中国 (GMT+08:00))To：Alexandra Zahradnikova <alexandra.zahradnikova@savba.sk>Cc：Tom Goddard <goddard@sonic.net> , 张晓飞<zhangxf@stu.ujn.edu.cn> , chimerax-users <chimerax-users@cgl.ucsf.edu>Subject：Re: [chimerax-users] (no subject)I think Sasha's advice is spot on here. If I try to generate just one model for the missing loops of the entire dodecamer, the job fails after running more than 5 hours because the maximum number of retries to get a status update is exceeded. The general procedure for what Sasha is suggesting would be: 1) Get a sequence viewer with only one of the chains associated. If you have a viewer with many chains associated, use that viewer's "Structure→Associations..." context menu item to reduce the associations to just one chain. Alternatively, you can open a viewer for just chain A with the "seq chain /A" command. 2) Use Modeller normally to generate a model for that chain with the loops filled in. 3) Generate 11 more copies of the filled chain with "combine" commands. 4) Use MatchMaker to align the copies onto the dodecamer chains. 5) Use the "combine" command again to combine the separate chain models into a single model. 6) If you don't like the chain ID assignments for the combined model, use the "Tools→Structure Editing→Change Chain IDs" tool to change them. --Eric Eric Pettersen UCSF Computer Graphics Lab On Sep 17, 2026, at 10:56 PM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi All, When I model missing loops in a homomultimer using Modeler, I always model just one monomer and then make copies and align them with the original monomers. Best regards Sasha Sent from my Galaxy -------- Original message -------- From: Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: 18/09/2026 02:45 (GMT+02:00) To: 张晓飞 <zhangxf@stu.ujn.edu.cn> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: (no subject) Here's Google's English translation of this inquiry: Dear Support Team, Hello. On September 14, 2026, I submitted Job L7VGGZ7PMNMYBWAR via the web service of ChimeraX 1.12. The task was a Modeller refinement to fill in the internal missing loops for the 9IM3 dodecamer (12 chains, ~4,800 residues). The job status returned as "failed". The stderr is empty, and the stdout cuts off midway through the bond angle violations list, with no models summary provided. While IL00010001.pdb and B99990001.pdb were generated, DL00010001.pdb is missing. In B99990001.pdb, all 12 chains are present with no missing residues; however, the residue numbering runs continuously from 1 to 6564 rather than being partitioned by individual chains. I suspect the job was forcefully terminated due to the computation time exceeding the server's single-task limit. Could you please clarify the following: Is there a maximum time limit per job for this service? For multi-chain tasks of this scale, do you recommend submitting them chain by chain? Can B99990001.pdb be reliably used as the final structure with the loops completed? I look forward to hearing from you. Thank you very much for your time and assistance. Best regards, On Sep 17, 2026, at 1:25 AM, 张晓飞 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: 您好： 我与2026年9月14日使用ChimeraX 1.12软件的web service中提交了Job L7VGGZ7PMNMYBWAR（modeller refine 补 9IM3 十二聚体 12 条链的 internal missing loops，~4800 残基）：status = failed，stderr 为空，stdout 在键角违反列表中途截断、无 models summary，IL00010001.pdb和 B99990001.pdb 存在但 DL00010001.pdb 不存在，其中 B99990001.pdb12条链都在，并无缺失残基，但是残基编号直接从1-6564，并未按链划分。疑似计算时长超过服务器任务上限被强制终止。请问该服务是否有单任务时限？此类多链任务是否建议分链提交？B99990001.pdb 是否可以作为补全残基后的结构使用？十分期待能够收到您的回复，谢谢。 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (5)
-
Alexandra Zahradnikova -
Eric Pettersen -
Tom Goddard -
Zach Pearson -
张晓飞