Zhanglab forum

Dear user, DeepMSA2 and DMFold can output paired MSA and single MSAs. you can find one example in DMFold example folder example/AF2Models/aMSA-aMSA/multi2.2-v4/seq/msas/paired.aln and example/AF2Models/aMSA-aMSA/multi2.2-v4/seq/msas/A DMFold itself accepts customs MSAs, and you can check details at ...

Dear user, It is possible that two-runs have different results with I-TASSER server, I-TASSER depends on templates, and the template library updates every week. You can always trust the one with a higher confidence score. BTW, if the model quality is not good, it is also possible that two-runs have ...

Dear Anu,

Your C-I-TASSER job IDs are CIT7972 and CIT7962, C-QUARK job IDs are QB3717 and QB3720, DeepFold job IDs are DF1540 and DF1545.

you can access the output at https://zhanggroup.org/C-I-TASSER/output/CIT7972/ as one example

Best Regards
Wei Zheng

Dear Anu,

Please let us what email you used, and I will send you the job IDs. BTW, we found some users' emails could not receive our email for unknown reasons (I also have this issue with one of my Gmail...), so I would suggest you change to another email next time.

Best Regards
Wei Zheng

Dear user,

What server have you used?

Best Regards
Wei Zheng

Dear user,

Yes, you definitely can use the results for publications, we would appreciate it if you could cite our TM-align work that appears on the website. Thank you.

Best Regards
Wei Zheng

Dear Gary, AlphaFold2 default pipeline indeed uses HHsearch to detect the template which will be one of the inputs, so it is correct for modeling. You are also correct if you do not want to use a template, you can set the seqcut parameter as 0, then the template features will be set as NA in the AF2...

Dear user,

The issue of your jobs has been fixed, and now it goes into the simulation step. We expect the jobs could be completed in the next 3-5 days. Let us know if you have any other issues or could get the results next week. Thank you for your bug reporting.

Best Regards
Wei Zheng

Dear user,

It is somehow related to our former library issue. But you can let me know the job ids, I will check if any issues with your jobs.

Best Regards
Wei Zheng

Dear Xilong, To speed up the modeling process, we fine-tune the maximal modeling MSA pair as 25 (scoring MSAs by M-score, see the paper for details), thus you get 25*5*5=625 models. The results you get are complete. While, if you want to generate more models, you can enlarge the cutoff from 25 to mo...