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23.5 FAQ Structure
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[ Convert PDB Chemical | Covalent bond | Write PDB | Renumber | Merge | Superimpose | RMSD | RMSD tips | delete residues | Atom distance | Ligand Pocket | Pocket conservation | Mutate Residue | Mutate Residue | Histidine Tautomer | Faq change torsion | Make Disulfide | read NMR | Solvent Accessible Area | weak hydrogen bonds | Formal Charge | Closest Neighbor ]

Questions and answers relating to protein and DNA structures, objects and the PDB

23.5.1 How do I change the bond types and add formal charges to a ligand from the PDB?


Please see the section in the cheminformatics chapter entitled Converting a Chemical from the PDB.

23.5.2 How do I make a covalent bond between a ligand and a receptor?


To make a covalent bond between a ligand and receptor:

Step one - place the ligand and receptor into the same object - how to move into one object is described here.

Step two - you can only make bonds in non-icm objects so you will need to "strip" the ICM object back to PDB Right click on the object name in the ICM Workspace and select Convert to non-ICM ...

Step three - use the ICM selection language to select the two atoms you would like to select and use the make bond command.

eg in 1f88 there is a covalent bond between the ligand retinal and K296 - zoom into it and see the bond - first we will delete this bond and then we will remake it like this:


delete bond a_1f88.aret/977/c15 a_1f88.a/^K296/nz

make bond as_graph

make bond  a_1f88.aret/977/c15 a_1f88.a/^K296/nz

If you right click on an atom it will give you the icm selection language for each atom.

23.5.3 How to write a pdb file?


23.5.4 How Do I renumber the residues in a PDB file


To renumber the residues in a PDB file you need to use the command line option

align number rs_residuesToBeRenumbered [ i_firstNumber ]

More details here:

http://www.molsoft.com/man/icm-commands.html#align-res-numbers

23.5.5 How can I merge two separate objects into one?


To merge two objects into one you can use drag and drop.

23.5.6 How do I superimpose two proteins?


The quick way to do this is described in the section entitled "How to Superimpose Two Structures". However more superimpose options are found in the Tools/Superimpose menu.

There are three options

  1. Superimpose two proteins by 3D only
  2. Superimpose two proteins
  3. Superimpose multiple proteins.

In option 2 and 3 above you can select exactly what you would like to superimpose e.g. backbone, Calpha. See the image below. Also you can select which protein you want to remain static.

23.5.7 How can I calculate the RMSD between two protein structures?


To calculate RMSD.

23.5.8 Can you give me some tips on which options to use for RMSD calculations?


There are a number of ways to calculate RMSD and the method you use depends on the problem you wish to solve. For example you need to use different approaches when calculating the RMSD of proteins and ligands.

There are two options in GUI:

  1. Tools/Analysis/RMSD # For protein structures only. http://www.molsoft.com/gui/rmsd.html
  2. Superimpose Button # will work for chemicals and protein structures but beware the ligand is superimposed and therefore not useful for comparing docked structures http://www.molsoft.com/gui/superimpose.html

Command Line:

  1. RMSD command http://www.molsoft.com/man/icm-functions.html#Rmsd
  2. Static RMSD command # the way to compare two docked structures - use the chemical parameter and beware of how many atoms have been compared when comparing non-identical chemical structures. http://www.molsoft.com/man/icm-functions.html#Srmsd

23.5.9 I would like to delete all the residues in my protein except for the ones surrounding the ligand binding pocket.


You cannot delete from an ICM Object. You can delete from a model or PDB structure. So if the structure is an ICM object strip it to a model by right-clicking on the name of the object in the ICM Workspace and selecting "strip". Now follow these instructions.

23.5.10 How do I display the distance between two atoms?


One way to do this is to use the atom select button on the right hand side of the graphical user interface.

More instructions on how to display distances can be found in the section of the manual entitled "Finding the Distance Between Atoms"

23.5.11 How do I display only the residues that surround the ligand binding pocket?


There is a quick and easy way to do this as described in the Tips section of the manual entitled "Quick Binding Pocket Display" or you may want to follow the instructions below for a more user-defined method.

For example if your structure is shown in ribbon you and you wanted to display the surrounding residues in xstick and udisplay the rest of the structure you would do the following.

Steps shown graphically below for the kinase 1ql6 and the atp ligand.

Step 1: Receptor (1ql6.a) is in ribbon display:

Step 2: Double click and select the atp molecule in the ICM Workspace

Step 3: Right click on the selected atp molecule in the ICM Workspace and select Neighbors. Enter radius and type of selection. Click OK and you will see a graphical selection of green crosses around the pocket.

Step 4: Convert your selection to a residue selection if you wish. You will then see green "R" in the graphical selection rather than green crosses.

Step 5: Select the xstick representation and the residues around the ligand will be displayed.

Step:6: If you want to undisplay the rest of the receptor outside the pocket use the invert selection button and then click the ribbon representation button.

23.5.12 How do I show the sequence conservation around the ligand binding site?


Here is an example of how to superimpose the structures of two proteins and display the sequence conservation around the ligand binding pocket.

PDB Search

NOTE: Please note that all alignments are linked with structure therefore selections can be made in the alignment. Also as an example structure can be colored according to the color in the alignment which is useful for identifying conserved regions.

23.5.13 How do I mutate a residue?


23.5.14 How do I mutate a terminal N or C residue?


Unfortunately with Internal Coordinates it is very difficult to re-route the first residue and last residue by using modify However there is a way around it which is a bit long but here it is:

For example we want to change the first and last residue of "1crn"


set tether a_2. a_1.

mncalls=10000

minimize "tz"
you should see the unfolded peptide thread onto the structure - if it is not 100% perfect repeate mn calls and minimize command

23.5.15 How do I change the tautomeric form of Histidine in a structure?


23.5.16 How can I change the torsion angle?


To do this:

23.5.17 How do I make a disulfide bond?


Use MolMechanics/Edit Structure/Set Disulfide Bond. More description of this can be found in the section entitled Making a disulfide bond.

23.5.18 How do I read in all the structures in a PDB file of a protein solved by NMR?



read pdb pdb_FileName all

e.g.


read pdb 1sgg all

23.5.19 How do I write a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein?


Here is a script to calculate solvent-accessible surface and tabulate the results to show area for each residue in a protein:


read pdb "1crn"
show surface area mute # compute surface areas
res = a_/1:18 # residue range of interest
n = Nof(res)  # the number of residues.
add column t Sarray(n, Name(Obj(res))[1]),Trim(Label(res),all),Area(res)

write t_1 separator="," "t.csv"  # read into Excel or something else similar

23.5.20 How do I display weak hydrogen bonds?


To display a weak hydrogen bond you may have to change the ICM parameter which controls the hbond strength threshold for hbond display. This parameter is called:


GRAPHICS.hbondMinStrength

By default it is set to 1 but the strength value can be set between 0. and 2. e.g By changing 1. to 0.2 you will see more weak hydrogen bonds.

23.5.21 How do I set a formal charge?


To set a formal charge:

  1. Display the molecule
  2. Simply right click on the atom and choose Edit---> Set formal charge.

23.5.22 How can I select the closest residue from the center of mass of a selected residue?


See the ICM language manual here :

http://www.molsoft.com/man/icm-functions.html#select-by-center-of-mass


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