Distance restraints for I-TASSER Problem

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UnknownUser
Posts: 3
Joined: Wed Jun 23, 2021 11:01 am

Distance restraints for I-TASSER Problem

Post by UnknownUser »

I have been trying to use the tool to predict the structure of a protein with distance restraints from in-vitro crosslinking data. I have tried to follow the instructions in https://zhanglab.dcmb.med.umich.edu/I-T ... raint.html for preparing the restraints .txt file and submitted several iterations. None of them seem to work and the restraints are not met in the output. Could anybody instruct us on how to submit the restraint .txt file correctly?


The pertinent job ID's are the following, see the first line in the restraint .txt file for clarification:

-S623936 (Tab-delimited)
DIST 216 CA 304 CA 9.8

-S624319 (Spaces identical to example)
DIST 216 CA 304 CA 9.8

-S624780 (Single-space-delimited)
DIST 216 CA 304 CA 9.8

Copy and pasted template from : https://zhanglab.dcmb.med.umich.edu/I-T ... raint.html
DIST 124 CA 84 CA 17.4

Note that these may look different dispayed on this post but if copied onto a txt document they are displayed properly.

Thanks for your help in advance!
xiaogenz
Posts: 71
Joined: Sun Apr 25, 2021 12:02 am

Re: Distance restraints for I-TASSER Problem

Post by xiaogenz »

One possible reason is that the weight of your provided distance constraint is less than that of the I-TASSER potential, since you just provided one residue pair.
UnknownUser
Posts: 3
Joined: Wed Jun 23, 2021 11:01 am

Re: Distance restraints for I-TASSER Problem

Post by UnknownUser »

Thanks for your quick reply xiaogenz, I have just posted the first restraint (/line) to show the formatting, but I submitted 23 restraints all with the same distance and all between alpha carbons like this:

DIST 216 CA 304 CA 9.8
DIST 79 CA 154 CA 9.8
DIST 118 CA 196 CA 9.8
DIST 59 CA 240 CA 9.8
DIST 304 CA 309 CA 9.8
DIST 211 CA 216 CA 9.8
DIST 312 CA 316 CA 9.8
DIST 216 CA 308 CA 9.8
DIST 304 CA 312 CA 9.8
etc.

(again the formatting here looks very different from the -txt file)
Thanks for your help again!
UnknownUser
Posts: 3
Joined: Wed Jun 23, 2021 11:01 am

Re: Distance restraints for I-TASSER Problem

Post by UnknownUser »

xiaogenz wrote: Fri Jun 25, 2021 3:37 am One possible reason is that the weight of your provided distance constraint is less than that of the I-TASSER potential, since you just provided one residue pair.
Thanks for your quick reply xiaogenz, I have just posted the first restraint (/line) to show the formatting, but I submitted 23 restraints all with the same distance and all between alpha carbons like this:

DIST 216 CA 304 CA 9.8
DIST 79 CA 154 CA 9.8
DIST 118 CA 196 CA 9.8
DIST 59 CA 240 CA 9.8
DIST 304 CA 309 CA 9.8
DIST 211 CA 216 CA 9.8
DIST 312 CA 316 CA 9.8
DIST 216 CA 308 CA 9.8
DIST 304 CA 312 CA 9.8
etc.
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