RE: It`s alive!!!

["Andrej Sali" <>]

I do not think there are examples exactly for your query in the manual. But
it should not be a problem to do it. There are several ways, one is outlined
here:

You could set the weights of all homology derived restraints to 0 using the
SCHEDULE_SCALE variable in SUBROUTINE ROUTINE = 'refine' or even 'refine_1'
or 'refine_3' (whichever you are using) (just copy it from
$MODINSTALL6v2/bin/__refine.top to the end of the main top file and edit it
accordingly).

I have not tried this, so please be careful since there may be 'little'
details lurking somewhere that can make your run go wrong ;-)

Best, Andrej

--
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and 
    California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier)
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232,  4233, 4239
Email ; Web http://salilab.org


> -----Original Message-----
> From:  
> [">mailto:] On Behalf Of Tom Duncan
> Sent: Thursday, February 27, 2003 6:29 AM
> To: Luis Rosales; Modeller_Usage
> Subject: Re: It`s alive!!!
> 
> 
> Luis & all Modellers -
> 
> OK, now that you've 'fixed' your problem, I think I've seen 
> this before as well. In my case, it happened when I had moved 
> my template PDB files from a PC to my SGI system, and 
> MODELLER did not like the DOS format of the files. With 
> nedit, if you open the file and then click "File" and "Save 
> As", it will have a checkmark by MS-DOS Format if that is the 
> case. Simply click that option OFF and save the file to 
> remove the DOS formatting.
> 
> PS - I'm still curious about a simple way to set up an MD 
> annealing run on a final model without any remaining 
> restraints from the template. Can the developers point me to 
> an example or guidelines in the manual?
> 
> Thanks & Happy Modelling,
> 
> Tom
> --
> Thomas M Duncan
> Research Associate Professor
> Dept Biochemistry & Molecular Biology
> Institute for Human Performance, Rm 4311
> SUNY Upstate Medical University
> 750 E Adams St
> Syracuse, NY 13210
> 
>