Search found 78 matches

by jlspzw
Mon Oct 03, 2022 10:27 pm
Forum: Main Forum
Topic: Clarification question about BioLip database
Replies: 4
Views: 33

Re: Clarification question about BioLip database

Dear user, Unfortunately, we didn't separate the RNA and DNA. But after you download the BioLip, you can find the pdb id for each entry. First, check the ligand ID NUC, then go to PDB and download the pdb/fasta based on pdb id for each entry. check the NUC ligand sequence. If the sequence contains '...
by jlspzw
Fri Sep 30, 2022 8:16 pm
Forum: Main Forum
Topic: No Result Obtained
Replies: 3
Views: 45

Re: No Result Obtained

Dear user,

you job has been completed https://zhanggroup.org/COACH/output/CH2099409567/

Best
IT team
by jlspzw
Fri Sep 30, 2022 5:52 am
Forum: Main Forum
Topic: Clarification question about BioLip database
Replies: 4
Views: 33

Re: Clarification question about BioLip database

Dear user, For 1, Yes, you are correct For 2, You may first download the entire BioLip and count them separately For 3, Unfortunately, you can only download the entire BioLip, which actually is not that large. For 4, Ligand ID: This can be the standard 3-letter code of ligand from PDB and MMCIF file...
by jlspzw
Tue Sep 27, 2022 8:54 pm
Forum: Main Forum
Topic: No Result Obtained
Replies: 3
Views: 45

Re: No Result Obtained

Dear user, Thank you for using our server. We found there are some communication issues between the job submitting server and the job running server, we are fixing the issue now. Please wait 1-2 days to see if the results come, we will monitor your job running and give you updates when it is complet...
by jlspzw
Sat Sep 24, 2022 10:07 pm
Forum: Main Forum
Topic: Inquires about the I-TASSER results
Replies: 1
Views: 59

Re: Inquires about the I-TASSER results

Dear user, I would suggest you download the pdb files of the two models from the results page and install pymol on your local computer. Then you can load the pdb files to pymol and use pymol to do this. You can also use the webpage, and go to the model section. right-click, then select console. then...
by jlspzw
Tue Sep 13, 2022 6:16 pm
Forum: Main Forum
Topic: Top 10 Templates for Domain Assembly
Replies: 1
Views: 132

Re: Top 10 Templates for Domain Assembly

Hi Our template library is PDB70, which is not an entire PDB, it takes a no-redundant PDB library with structure similarity cutoff TM-score=0.7. So it is possible that your native structure is not in the library. Since our library is not based on sequence similarity, so it is possible that the picke...
by jlspzw
Wed Sep 07, 2022 9:15 pm
Forum: Main Forum
Topic: Please make sure the directory /tmp/ is writable for you
Replies: 2
Views: 197

Re: Please make sure the directory /tmp/ is writable for you

Hi 1 Please check if you have folder /tmp/cflcyd? 2 If yes, then try to do something in /tmp/cflcyd, for example cd /tmp/cflcyd; touch test.txt; echo "aaa" >test.txt see if /tmp/cflcyd is a writeable folder, normally a folder with 777 permission should be OK for writing data. If no, try to...
by jlspzw
Fri Sep 02, 2022 7:03 am
Forum: Main Forum
Topic: Information regarding restraint files generated and used by I-TASSER standalone program
Replies: 1
Views: 299

Re: Information regarding restraint files generated and used by I-TASSER standalone program

generally, comb*.dat are contact restraints from the templates, dist*.dat are distance restraints from templates. combCA.dat and distL.dat comb8CA.dat are CA contact or distance.,comb.dat and dist.dat are side-chain center contact and distance. combCA.dat are contacts with distance<6A, comb8CA.dat a...
by jlspzw
Thu Aug 18, 2022 9:53 am
Forum: Main Forum
Topic: 3DRobot standalone package availability
Replies: 2
Views: 388

Re: 3DRobot standalone package availability

Dear user, I don't have any issue when downloading the 3DRobot package at http://zhanglab.dcmb.med.umich.edu/3DRobot/download/3DRobot1.0.tar.bz2; some browsers will report the bz2 file as dangerous file and block it, so you can check with other browser or check if your anti-virus software block it. ...
by jlspzw
Tue Aug 16, 2022 6:10 am
Forum: Main Forum
Topic: No confirmation email received from C-QUARK and C-Ethreader after job submission
Replies: 4
Views: 489

Re: No confirmation email received from C-QUARK and C-Ethreader after job submission

Dear user,

Your C-QUARK job should be https://zhanggroup.org/C-QUARK/output/QB2232/ and CEthreader job should be https://zhanggroup.org/CEthreader/output/CEC509/

It seems those two are submitted today, if you have ever submitted before, I didn't find them at our database.

Best
IT team