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Re: MODELLER and external constraints (such as NMR)

Dear Andras:

     Many thanks for your help. After I got your message, I spent these
two days to understand the manual and examples that you pointed out.  I
followed Examples 9 and 10 (page 106-107, manual) to take a test, but
have not succeeded yet. The following are my new questions:

    (1) Variable name not recognized: RESTRAINED_ATOMS in example 10.
    (2) Variable name not recognized: ALIGNMENT_FILE,  but it works with
    (3) The log file of example 9 gave a error message "rdcsr1___E>
wrong key:  ".
    (4) Does examples 9 use both homology-derived restraints and
user-added constraints in modeling? I have a hard time to understand
that "ADD_restraints" is "off"(page 84, manual). If yes, what is the
difference between example 9 and 10? in the restraint file? 

    (5) What is the difference between Group 28 and Group 29 on page
74?  both are NMR distance constraints.

    (6) NOE-derived distance constraints are usually specified in terms
of a distance range, what is the best form for thse constraints in
MODELLER (page 73, manual)? 

    (7) Equation (6.59) on page 129 could have typo in conditions.

    (8) If external constraints contradict with the homology-derived
constraints, what will happen and what should we do?

     I am sorry to give you a long list of questions. I would greatly
appreciate your help.


Best regards,

Chunhua Yuan

Andras Fiser wrote:
> Hi,
>  please look at the ADD_RESTRAINTS command. With that one you can add your NMR
> distance restraints or any kind of the 31  available other restraint types. The
> parameter format is discussed in the manual "Specification of restraints"  in
> 2.5. Examples are given in the command discussion of ADD_restraints. Also
> please look at Freq. Asked question in the manual: example 8,9,10,11.
> best wishes
> Andras