PyMOL scripts

PyMol script files are provided to display coordinates and align chains and Pfam domains. They are included in all downloadable coordinates files, including chain interfaces, domain interfaces, Pfam-peptide interfaces and Pfam-ligands interactions.

Pymol script files in chain interface clusters

You can make a simple multiple alignment of interfaces in a cluster by Pymol. The Pymol Script files (with extension .pml) are included in the interface cluster tar.gz file. After you unzip the the interface files, double click the Pymol script file, the interfaces are displayed by aligning all other interfaces to the first interface. The first interface is selected because of best resolution with least missing coordinates. There are two Pymol script files: GroupID_ClusterID.pml and GroupID_ClusterID_bychain.pml.

The GroupID_ClusterID_bychain.pml script alignes chain A of each dimer to chain A of the first structure, e.g., align 1bcd_1.cryst and chain A, 1abc_1.cryst and chain A

Sometimes the structure alignments may look better if both chains are aligned at same time (GroupID_ClusterID.pml), e.g. align 1abc_1.cryst, 1bcd_1.cryst

Please note that the alignment uses the default structure alignment of PyMOL program, and is only for your convenience. In some cases, the alignments are not working very well, manual adjustment is necessary.

(Pkinase)_(Pkinase_C) chain cluster 1 aligned by chain A

(Pkinase)_(Pkinase_C) chain cluster 1 aligned by dimers (both chains)

Pymol script files in domain interface clusters

• GroupID_ClusterID_chain.pml is to display domain interfaces in whole chains. The domain segment is colored by "rainbow", the segments other than the domains are colored in gray. If you want to change to different colors, you need modify the related PyMol command lines in the script file or modify in PyMol program. The following picture shows the first domain cluster of ACT domain. ACT domain is shown in rainbow, the segments other than the domains are colored in white.
  
• GroupID_ClusterID_chain_rep.pml is similar to "GroupID_ClusterID_chain.pml", but only display domain interfaces in representative structures. This is useful when it is a large group containing many structures.
• GroupID_ClusterID_domain.pml is to display just domain interfaces without showing whole chains. The coordinates of remaining chains are still loaded, just hidden. ACT domains are colored in rainbow.
  
• GroupID_ClusterID_domain_rep.pml is similar to "GroupID_ClusterID_domain.pml", but only display domain interfaces in representative structures.

Pymol script files in Pfam-peptide interfaces and clusters

Coordinates of a Pfam and peptides

The file can be downloaded on the Pfam page, is named PfamID_pep.tar.gz (e.g. Bromodomain_pep.tar.gz). After untar the file, there are four PyMOL script files.

• _byChain.pml is aligned by domains in default mode of PyMOL, but display the entire chains. The segments other than the domains are colored in white. The peptides are colored in magenta.
• _byDomain.pml is aligned by domains in default mode of PyMOL. Display only the segments of domains.
• _pairFit.pml is aligned by domains based on this Pfam hidden Markov mode positions, but display the entire chains.
• _pairFitDomain.pml is aligned by domains based on the hidden Markov mode (HMM) positions of the Pfam, but display only the segments of domains.

All domains are colored in rainbow, from blue to red, from N-terminal to C-terminal. The color can be changed either by modifying the PyMol script files or using commands in PyMol program.

Trypsin and all peptides

Coordinates of a cluster of a Pfam and peptides

The file can be downloaded on the Pfam page, is named PfamID_pep.tar.gz (e.g. Bromodomain_pep.tar.gz). After untar the file, there are four PyMOL script files.

• PfamID_ClusterID_byChain.pml is aligned by domains in default mode of PyMOL, but display the entire chains. The segments other than the domains are colored in white.
• PfamID_ClusterID_pairFit.pml is aligned by domains based on the hidden Markov mode (HMM) positions of the Pfam, but display only the segments of domains.

The first cluster of Trypsin-peptide interfaces

Pymol script files in Pfam-ligand interactions

There are two types of coordinates for Pfam-ligand interactions for downloading: one Pfam and its interacting ligands and one ligand and its interacting Pfams. Different Pymol scripts are compiled into the coordinate files. Please go to Pfam-ligand help page for details.