BALBES References

Please cite the following paper in any publication arising from use of BALBES:

F.Long, A.Vagin, P.Young and G.N.Murshudov "BALBES: a Molecular Replacement Pipeline " Acta Cryst. D63 (2007) (accepted for publication)

Run BALBES

1. Run BALBES from command lines
2. Run BALBES in ccp4i
3. Run BALBES in our web server

1. Run BALBES from command lines

It is very simple to run balbes under linux and MacOS. It involves typing the program's name and a few key words. Typical command line is :

balbes -o a_directory_name -f a_structure_factor_file_name -s a_sequene_file_name

Explain

1. program name: balbes

2. key words (include symbol - ):

-o (optional) ------- following by the name of the directory into which you want to put all of the output generated by balbes.
e.g. -o MyjobOne
or -o ../output_abcd

If the directory does not exist, the program will create the directory( MyjobOne, or ../output_abcd) for you.

Furthermore, the prgram will create a few subdirectories under the above directory, e.g.

process_details -- stores all *.log, *.ps files, which record the details during executing balbes.
results -- stores the final solutions in terms of pdb and mtz files.
template_models--contains all candidate models found.

If -o is omitted, the program will create a output directory called output_username (e.g. output_fei)

-f (required) ------- followed by the name of a structure factor file. The file could be a .mtz file or a .cif file.
If the file is in the current directory, you can just type name, e.g,
-f 1ab2.mtz
or -f 3cd4.cif
Otherwise you need to input the file name with the absolute path. e.g,
-f /home/dir1/dir2/1ab2.mtz
or -f ../3cd4.mtz
-s (optional) -------- followed the name of a sequence file. You can find the format of a sequence files containing one sequence or multiple sequences

Depending on where the file is,it can be,

-s aaaaa.seq
or -s ../../aaaa.seq
or -s /Users/abcd/data/aaaa.seq
-m (optional) ------- followed by the name of a pdb file. This pdb file will be used as the user's input candidate model for molecule replacement. Once keyword "-m" can be used with and without "-s" (with or without sequence file). BALBES will not search its own internal database for MR candidate models if key word "-m" is used.
If the pdb file is in the current directory, you can just type name, e.g,
-m myOwnPdb.pdb
Otherwise you need to input the file name with the absolute path. e.g,
-m /home/dir1/dir2/xxxxx.pdb
or -m ../3cd4.pdb
-l (optional) ------- followed by the name of a directory which contains a group of pdb files. This directory will be used as a user's database. BALBES will look into this directory to find the candidate models for molecule replacement. Once keyword "-l" is used, BALBES will not search its own internal database for MR candidate models. You need to use "-l" and "-s" at the same time.
For example,
-l myLib/ -s a_sequence_file_name
where in myLib, there are a group of pdb files

3. Examples

A) Input both a structure factor file and a sequence file
a) balbes -o output_1ab2 -f 1ab2.mtz -s 1ab2.seq
That means:
1. balbes will create a directory 'output_lab2' under the current dirctory. 'output_lab2' contains a few subdirctories which store all output from balbes.
2. The input structure factor file, 1ab2.mtz, and sequence file,1ab2.seq, are both in the current directory.
b) balbes -f 1ab2.mtz -s 1ab2.seq
That means:
1. You has not assigned a root directory for your job. balbes will create a directory 'output_your_user_name' under the current dirctory. 'output__your_user_name' contains a few subdirctories which store all output from balbes.
2. The input structure factor file, 1ab2.mtz, and sequence file,1ab2.seq, are both in the current directory.
c) balbes -o /home/abcd/ef -f /home/abcd/other_dir/1ghij.mtz -s ../2lmn.seq
That means:
1. balbes will create a directory 'ef' under the directory '/home/abcd/ef' contains a few subdirctories which store all output from balbes.
2. The input structure factor file, 1ghij.mtz, is in '/home/abcd/other_dir/', and sequence file,2lmn.seq, is in '../'. Both files must exist.
B) Use your own model pdb file. Input both a structure factor file and a pdb file. Using a sequence file is optional in this case.
balbes -o output_XXXX -f xxx.mtz -m xxxxx.pdb (optional : -s xx.seq)
That means:
1. balbes will create a directory 'output_XXXX' under the current dirctory. 'output_XXXX' contains a few subdirctories which store all output from balbes.
2. The input structure factor file, xxx.mtz, and model pdb file, xxxxx.pdb, are both in the current directory.
3. xx.seq will be used if "-s xx.seq" is presented

C) Use your own database consisting of a group of pdb files. You need to input a structure factor file, a directory containing the pdb files and a sequence file.
balbes -o output_XXXX -f xxx.mtz -l myOwnLib/ -s xx.seq
That means:
1. balbes will create a directory 'output_XXXX' under the current dirctory. 'output_XXXX' contains a few subdirctories which store all output from balbes.
2. The input structure factor file, xxx.mtz, and sequence file, xx.seq, are both in the current directory.
3. you put all your pdb files to searched in the directory myLib/

2. Run BALBES in ccp4i

1. Start 'ccp4i' by typing ccp4i
2. From module list, select Molecular Replacement
3. From 'Molecular Replacement' list, click BALBES. The BALBES task window will jump out.
4. Fill all items in BALBES task window, which are self-explained. Then click 'Run' manual and select Run Now. BALBES will start to work for.
5. Other steps (such as view the results) are standard procedures in ccp4i. Please consult with ccp4i's help manual if you are not familiar with them.
6. Using your own model pdb file or your own pdb database is only available from the command line and will in ccp4i soon.

3. Run BALBES in our web server

• Go to our web server and register. Then you can run BALBES in the web server

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