The problem hasn't been solved
Hi friends,
I want to modeling my antibody by webserver of rosetta antiboy, but I faced with the error:
ERROR: Current DB does not cover the length of FRL of your query. ERROR: FRL length of your query: 59 ERROR: DB: 58 or 60
Would you help me to solve the error?
Hi all,
So I have been trying to stitch homology models together using Remodel and when it stitches the stitched piece often ends up clashing with the structure it is stitched onto. I am using the following command:
remodel.linuxgccrelease -s model3.pdb -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -save_top 1 -overwrite -out:file:scorefile model3.sc -run:chain A >> model3.out
Hi,
here is the command I used. When I set num_packs to 1 which is the default value, the program runs pretty fast, when I set it to other values, the program is stuck there. The version is rosetta 3.6.
Hi,
I'm trying to implement FeatureReporters in PyRosetta (compiled from release 3.5). I'm implementing the following methods:
Both of these methods get utility::sql_database::sessionOP as input. When I try to run the code I get the following error message:
I submitted a Heavy and lIght chain sequence with and without the 'multiple template grafting' and H3 loop modeling and recived the same errors each time- "Chothia numbering of FR_L1".
Does anyone know how to get around this error so that the antibody will be modeled? job #'s 24670, 24671
thank you
Hello, everyone!
I have maybe quite a silly question. What is the best methodic of homology modeling when my template and target have quite different lengths. Like target has 350 and the second has 260. Shall I just get rid of some tail part of longer protein during alignment? And yes, it seems that this is the best homolog for my type of protein.
Hello Everyone,
While trying to use harmonic, or guassian, distance restaints in low resolution centroid only docking in the docking_protocol.linuxgccrelease I've encountered weird Scoretype: atom_pair_constraint score errors that prevent the output of docked proteins.
Dear all,
I built a model for a membrane protein and know I try to refine a long extracellular loop using NG-KIC modeling. I noticed that some sgments can reach the outer transmembrane space. I am trying now to use constraints to penalize this behaviour. In your opinion what is the best type of constraints I can use to achieve this.
Regards
Hi everyone,
I'm attempting to use a script involving a number of different components, but have run into a certain issue.
When I intiate the mover using the attached XML file "design.txt" (which is renamed design.xml when running the script), I get an error of:
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - pack=======================
Illegal instruction
The full log is attached (designerr.log).