Re: MODELLER and external constraints (such as NMR)

[Andras Fiser <andras@tuba>]

Hi Chunhua,

> 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.

following your example, please replace your line in file p15_test2:

SET RESTRAINED_ATOMS = 'CA' 'CA', RESIDUE_IDS = '2' '10'

with 

set ATOM_IDS =  'CA:2' 'CA:10'

for me it works now.


Your other top file, which reads the restraints, directly from a file, looks as
if it is OK. You did not write any problem, I hope it works for you as well.

>     (2) Variable name not recognized: ALIGNMENT_FILE,  but it works with
> "ALNFILE".
> 
>     (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?


ADD_retsraints =off means everything is to be deleted whatever was before, and
use the new, actually read restraints (in this case -example 9 - this is the 
default CSRFILE). When you read the my-rsr1.rsr than you set ADD_RESTRAINTS=
on, because you wish to keep the CSRFILE >and< add this new one. etc.

MODELLER automaticly derives angle, dih angle, distance etc etc restraints
during its run, which by default are used during the optimization.

You have several choices: you can say, that you do not need any of the
automaticly derived restraints, because you want to use only your own
restraints: example  11.

In your case there is an other situation (if I am correct): you wish to keep
the automaticly derived restraints and add your new ones from NMR experiments.
You can do it in two ways: If you have only a few one you can include them in
the top file (example 10) or if you have let's say a few hundred than it is
better to create and read in the new , additional restrains from a file or from
files. (example 9)


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

Basicly nothing, this is only to document your restraint file: there is no
difference if you choose any of them even if you choose  1 or 27 etc. But it is
a good idea to annotate your new restraints corrdctly, e.g. as 28 or 29 because
than they will be listed in that row in the restraints table that is reported
in the log file. So you can see the summary of your restraints,as a fast
check,  if they are included or not.

>     (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)?

Probably the  best in case of NOE to define an upper limit ( form 2 page 74)
because that is what you usually know from NOE.  

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

well, It looks to me that the third condition may be incorrect , we will check
it.

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


Modeller will try to optimise all the restraints simultaneously. In the Log
file you will see the violated restraints if you see serious contradiction it
is better to remove some of the restrains.

When Modeller5 is released, probably there will be a more up-to-date manual as
well.

I send this message for modeller_user group as well.

Best wishes

Andras