Zhanglab forum

Dear user, Thank you for raising this question. We have two kinds of contacts, contacts between CA atoms, and contacts between CB atoms, so in the contact map figure, we have 2 before LxL, similar to the distance map, we have CA distance and CB distance. For distance prediction, we did not directly ...

Dear user, The server usually sends the results back to the user in around one week. However, we recently received around 1200 submissions, so the server is overloaded. We are trying to move the jobs to a larger supercomputer cluster, we are expect the current submitted jobs will completed one by ...

Dear user,

We also have a single sequence size limitation, which was 1200 before; I just slightly increased it, so you can submit it now.

Sheng Regards
Wei Zheng

Dear user, We recently got>1000 submissions from the user community, which is overloading our server. So, the job response time is much longer than usual. We are trying to seek new resources to solve the problem. However, we still need time to set up everything. I have cancel your old job, now you ...

Dear user,

Please put the sequence here; I will help you check the case.

Best Regards
Wei Zheng

Dear user,

You can try https://zhanggroup.org/DMFold/, put two copies of your monomer sequences, and then it is dimmer.

Best Regards
Wei Zheng

Dear user,

Your change is correct. Please let us know if you have any questions.

Best
Wei

Dear user, DeepMSA2 doesn't contains aMSA, the readme file has some typo, we will delete it from readme. DeepMSA_IMG.py does not require aMSA. qMSA and dMSA is enough for next step. if you only have qMSA.hhb* dMSA.hhb* and do not have d/qMSA.jac* and others, DeepMSA_IMG.py will tell you no need to ...

Dear user,

You can check the config.py, see the dMSA_cpu setting, etc.

Please try to reduce the CPU number to see if memory can be reduced.

BTW how large is your memory on your Desktop, and how large are your sequences?

Best Regards
Wei Zheng

Dear user, You are encouraged to use https://zhanggroup.org/DMFold/ or https://zhanggroup.org/D-I-TASSER/ servers. When using D-I-TASSER, please try to select those three options. Using large IMG/JGI metagenomic database to build MSA (additional one or two days maybe applied). Using AlphaFold2 ...