Structure Calculation Using CS-Rosetta: Difference between revisions
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== ''' | == '''Introduction''' == | ||
The CS-ROSETTA approach (Ref. 1,2) combines the Monte Carlo based structure assembly program ROSETTA with empirical structural information obtained from backbone and <sup>13</sup>Cb chemical shift data. The robust CS-ROSETTA protocol is capable of successfully predicting 3D protein structures up to 15 kDa in size (Ref. 1). A complete description of the program along with downloads are available from the Bax laboratory web site: | |||
http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html | http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html | ||
Perform flexible region prediction on the [http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_e.py RCI Web Page]. | |||
=== '''Random Coil Index Prediction''' === | |||
Perform flexible region prediction on the [http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_e.py RCI Web Page]. | |||
RCI will take a bmrb file in the old format, as produced by CYANA 1.0 (the new BMRB format has an extra "chain" column). Unlike AutoStructure input file, the sequence field should be left in place. | RCI will take a bmrb file in the old format, as produced by CYANA 1.0 (the new BMRB format has an extra "chain" column). Unlike AutoStructure input file, the sequence field should be left in place. | ||
Use an init.cya file: | Use an init.cya file: <nowiki> | ||
<nowiki> | |||
name:=XXXX # Replace XXXX with NESG ID | name:=XXXX # Replace XXXX with NESG ID | ||
cyanalib # Read the standard library | cyanalib # Read the standard library | ||
pseudo=2 # Allows HB, HD, etc. pseudoatom names, use with CARA | pseudo=2 # Allows HB, HD, etc. pseudoatom names, use with CARA | ||
read seq $name # Initialize | read seq $name # Initialize | ||
</nowiki> | </nowiki> | ||
If you are using proton list from CARA, convert it first to "dyana" format with Cyana 2.1: | If you are using proton list from CARA, convert it first to "dyana" format with Cyana 2.1: <nowiki> | ||
<nowiki> | |||
read prot XXXX.prot | read prot XXXX.prot | ||
pseudo=0 | pseudo=0 | ||
translate dyana | translate dyana | ||
write prot XXXX_dyana | write prot XXXX_dyana | ||
</nowiki> | </nowiki> | ||
Use cyana 1.0.5 to prepare a bmrb file | Use cyana 1.0.5 to prepare a bmrb file <nowiki> | ||
<nowiki> | |||
read prot XXXX_dyana.prot | read prot XXXX_dyana.prot | ||
bmrblist XXXX.bmrb | bmrblist XXXX.bmrb | ||
</nowiki> | </nowiki> | ||
Make sure you change the <tt>_Chem_shift_ambiguity_type</tt> tag to <tt>_Chem_shift_ambiguity_code</tt>. Yes, it is stupid, but RCI will report an error if you don't do it. | |||
Flexible N- and C-terminal tails should be removed for CS-ROSETTA calculation to reduce CPU time. Flexible loop regions will later be excluded from calculation of all-atom energy. | |||
=== '''Generating MFR fragments on U2 cluster at SUNY Buffalo''' === | |||
Copy the <tt>runCSRjob.com</tt> file into the working directory and change the number of fragments to be generated. | |||
Type <tt>qsub runCSRjob.pbs</tt> to submit the job into queue. This calculation takes ~2 hours for 1000 fragments for a small protein, therefore it cannot be run on a master node. | |||
=== '''Running CS-Rosetta on U2 cluster at SUNY Buffalo''' === | |||
Go to the <tt>rosetta</tt> subdirectory. Figure out how many parallel Rosetta jobs you will need to run. Things to consider are: | |||
*The total number of fragments to be calculated | |||
*The maximum wall-time for a single job is 72 h | |||
*It takes ~10 min to calculate a single structure of a small protein on a single CPU | |||
Type <tt> | <br> Type <tt>./runRosetta.csh N</tt>, where =N= is the number of parallel Rosetta jobs | ||
-- AlexEletski - 17 Apr 2008 | |||
-- | -- Updated by JimAramini - Nov 2009 | ||
Revision as of 17:29, 6 November 2009
Introduction
The CS-ROSETTA approach (Ref. 1,2) combines the Monte Carlo based structure assembly program ROSETTA with empirical structural information obtained from backbone and 13Cb chemical shift data. The robust CS-ROSETTA protocol is capable of successfully predicting 3D protein structures up to 15 kDa in size (Ref. 1). A complete description of the program along with downloads are available from the Bax laboratory web site:
http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html
Random Coil Index Prediction
Perform flexible region prediction on the RCI Web Page.
RCI will take a bmrb file in the old format, as produced by CYANA 1.0 (the new BMRB format has an extra "chain" column). Unlike AutoStructure input file, the sequence field should be left in place.
Use an init.cya file: name:=XXXX # Replace XXXX with NESG ID cyanalib # Read the standard library pseudo=2 # Allows HB, HD, etc. pseudoatom names, use with CARA read seq $name # Initialize
If you are using proton list from CARA, convert it first to "dyana" format with Cyana 2.1: read prot XXXX.prot pseudo=0 translate dyana write prot XXXX_dyana
Use cyana 1.0.5 to prepare a bmrb file read prot XXXX_dyana.prot bmrblist XXXX.bmrb
Make sure you change the _Chem_shift_ambiguity_type tag to _Chem_shift_ambiguity_code. Yes, it is stupid, but RCI will report an error if you don't do it.
Flexible N- and C-terminal tails should be removed for CS-ROSETTA calculation to reduce CPU time. Flexible loop regions will later be excluded from calculation of all-atom energy.
Generating MFR fragments on U2 cluster at SUNY Buffalo
Copy the runCSRjob.com file into the working directory and change the number of fragments to be generated.
Type qsub runCSRjob.pbs to submit the job into queue. This calculation takes ~2 hours for 1000 fragments for a small protein, therefore it cannot be run on a master node.
Running CS-Rosetta on U2 cluster at SUNY Buffalo
Go to the rosetta subdirectory. Figure out how many parallel Rosetta jobs you will need to run. Things to consider are:
- The total number of fragments to be calculated
- The maximum wall-time for a single job is 72 h
- It takes ~10 min to calculate a single structure of a small protein on a single CPU
Type ./runRosetta.csh N, where =N= is the number of parallel Rosetta jobs
-- AlexEletski - 17 Apr 2008
-- Updated by JimAramini - Nov 2009