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.

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
• the SRS 3D server
• VMD

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, what could be a result of technical problems with the X-ray diffraction data (more frequently). To overcome this error, the first step should be to identify its source. For that, a fasta sequence can be generated from the PDB file containing the coordinates (it should be a simple script, or even a couple of command lines, but if any help needed, please write an email to bitar@rostlab.org). After this, align this sequence with the fasta sequence for the same protein and check for missing residues (gaps within the alignment). If residues are missing, simple remove those from the original sequence and generate a new alignment between template and target.

SNAP

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

Build_mutation Script --> dead simple python script that creates a complete mutation file (including A to A mutations) for snap2. Does not work with SIFT web server as only one mutation per amino acid position is regarded.

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.