P.S. just one extra question: I noticed a small bug in the order of amino acids added by the modeller in the case where they are added in the N-terminal positions. For example, if 10 amino acids are added in the first position, they will be numbered in the sequence like -10,-9 ... 0, and than 1,2,3 (for residues that were in the original pdb). Do we need to use a special save command for the generated model something like: save test.pdb #2.1 + some specific options ? Many thanks in advance Enrico Il giorno mar 27 ago 2024 alle ore 12:15 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
So it seems that I could resolve the issue in the following manner. For the system contained 4 chains I opened all sequences
sequence chain /R Alignment identifier is 1/R sequence chain /B Alignment identifier is 1/B sequence chain /A Alignment identifier is 1/A sequence chain /G Alignment identifier is 1/G
and then run prediction of all missed fragments for ALL 4 chains, which produced at leas the model without steric clashes.
ui tool show "Model Loops" modeller refine 1/A:1:all-missing 1/B:1:all-missing 1/G:1:all-missing 1/R:1:all-missing numModels 1 fast true adjacentFlexible 1 protocol standard
Il giorno mar 27 ago 2024 alle ore 09:44 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Thank you very much Elaine !
Actually I've tried to follow this but modeller did not work in that case.
Briefly, to be clear I need to model only one chain (A) in my complex but considering the presence of other chains in order to omit any sterical clashes between newly built residues and other chains. So having all complex loaded in chimera-X window I loaded sequence for the chain A seq chain /A and then as it was mentioned associated it to the whole complex sequence associate #1
Then I run modeller from the GUI which indicated a problem in the alignment file
Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 8hti_1
Il giorno lun 26 ago 2024 alle ore 23:42 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window.
The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico