Resource software

Here, we collect descriptions of the software used in the practical. This can be software used in online portals or software installed locally on your own computers or the lab resources. In each case, please describe how to access the software and where to find manuals. Also use this site to collect scripts or HOW_TOs that could be useful for others.

Your own scripts

If you have produced a script that does something that could be useful for others, please "publish" it here. E.g. create a page for your tool where you provide information where to find the software (path on the student cluster, git repository, ...) and how to use it. -- For users: If you use a script produced by another group, please document that (e.g. in the "lab book" part of your wiki section). And if you find bugs, please help the other group improve.

A script for executing blastp, blastpgp and hhblits with different databases and number of iterations (also using checkfiles for blastpgp and outputting the PSSMs): Media:run.pl

Molecular visualization

To look at protein structures you can use any molecular visualization programm. Here are a few options:

• PyMOL -> installed on the i12k-biolab computers
• Jmol, e.g. via PDB
• VMD
• the SRS 3D server -- unfortunately not working any more. Maybe Aquaria will become publicly available within this practical.

Changing Blast output

By default, Blast lists 500 search hits and 250 alignment details. This can be changed (see Blast manual for details):

• You can use a custom output format to get a table with "-m 8" (see "-help" or this hint on how to parse Blast output).
• You can use "-b" to set the number of alignments to be shown, "-b 20000" is the maximum.

Modeller

Troubleshooting

A very common error from Modeller is the following: "Sequence difference between alignment and pdb" . This usually means the structure of the template available in PDB (which was experimentally solved) has missing residues, which could be a result of technical problems with the X-ray diffraction data. Therefore, you need to make sure sure target-template alignment uses the sequence implied in the ATOM records, not the SEQRES record. To locate the error you could e.g. generate a fasta sequence can be generated from the PDB file coordinates, align this sequence with the fasta sequence for the SEQRES sequence and check for missing residues (gaps within the alignment). If residues are missing, regenerate you target template alignment based on the new fasta sequence made from the coordinates.

SNAP

There is a very brief explanation about SNAP available here --> Media:SNAP.pdf.

Energy Minimization

There is a script to automatically run energy minimizations with Gromacs here --> MutEn.pl.

R

Error in hist.default(a$V2, main = "evals") : 'x' must be numeric

Blast uses non-standard scientific notation and ommits the preceding 1 for eValues like 'e-190'. Change it to '1e-190' and R will stop complaining.