The Morphinator Guide
Presentation: Introduction To Morphinator
Presentation: The Morphinator quick start guide
What will you get?
You will receive a multistage PDB file which can be viewed as a trajectory in the embeddded NGL viewer on this page. In addition you can download the multistage PDB file and every step.
The files can be further processed in rendering programs to make films. Though later on we will offer a simple online movie maker derived from NGL viewer. You can add B-fac visualization
as vibrations to the structure.
The principle idea behind Morphinator
The principle idea behind old school morphs was to linearly transform the protein atoms from A to B. Usually A and B are crystal structures and the intermediates are 'fictive steps'.
From these number of intermediates a quick film can be produced to visualize the protein dynamic behaviour of the protein.
The linear transformations were problematic as we would introduce steric clashes resulting in impossible energy requirements at room temperature.
In other words the produced films were highly unrealistic. Jesper Karlsen improved this by adding a geometric minimization through the phenix module for each step. This meant that the
transformation satisfied some basic constraints. The basic assumption in Morphinator is thus that any trajectory which transforms the protein from A to B will take the shortest possible path
satisfying forcefield constraints. This is obviousely not the entire truth as people who have professsions molecular dynamics would know, though as we will demonstrate in our article
the assumption imitates closely the real behaviour of the protein.
Creating your first morph film
The first thing you do is press "Add PDB to sequence.". You will now see a textfield has been added. In the textfield called "start PDB" we will add the name of the pdb
file you morph from (try 9b3b) and the PDB file text field you add the PDB to morph to(try 9b3r). The pdb files will be downloaded from the pdb database. If you have a custom
made PDB file you simple upload it and its name will appear in the txt field. You can manually type the name into the textfield of your uploaded pdb file
but be carefull it must have exact file name(name + extension e.g "Mypdb.pdb"). Morphinator also accepts .cif files. The "Steps" textbox you type the number of steps
to transform from A to B. Generally the more steps the smoother. Normally we recommend 20 steps.
Now you simple write the name of the results file plus the file extension: .pdb. Currently morphinator can only produce .pdb files. Press submit and you will
be taken to the next page after processing (usually takes 1-5 min.). This page tells you what residues have been moved as A and B must have same residues, all the wise residues will "magically" appear and dissapear
in the film. If you are satisfied press submit and the log box will monitor the progress and report back to you. Once complete a download buttom will appear or you can press "view with NGL" view
to watch the film in your browser.
Optional fields and good to know
The optional txt fields are blue. The tick boxes are ofcourse also optional.
The Model textfield
If you have a multistage PDB file, usually due to the data is collected from an NMR then you can select which PDB model you wish to use. If you do not select a model then
default is Model 0.
Delete field and upload file
You are required to delete the field with "delete field" buttom if left unused. We decided to add the upload buttom since people could potentially customely add ligands and see the
ligands move around the morph animation which was not originally in the PDB file. In addition if the PDB file is unpublished then it does not exists in the PDB databank.
Crop to previous tickbox
If you have a large PDB sequence of e.g. 12 steps and you want ligands to spawn and vanish from the PDB file then the tickbox is worthwhile. If left checked then imagine
a sequence A, B and C. Then we check C, it will only crop out residues which are not present in B, pr. default it will also crop out residues not in A.
Acceleration value
Due to morphinator has no time dimension you can put the number of steps proportional to each other to illustrate the rates for each step. Unfortunately the coordinate transformation
is linear. By addind the Acceleration value we can speed the transformation up or down over the morph. If < 1 then the transformation starts at a fast pace and slows down and if 1 <
it starts slow but speeds up. If i only want this to happend for an arbitary amount of steps (say we have 20 steps all together) then write 1-10,0.9,11-20,1.... (1-10 are the steps), 0.9
is the acceleration factor and 11-20 is the remaining steps and 1, is the default value indicating no acceleration happends what so ever.
Superpose to
This mostly allways has to be done in either Morphinator or in an external program. Often the proteins are in two unique coordinate systems so they must be aligned. You can
superpose to a PDB file in the morph seqeunce or something else from the protein databank or upload your own PDB file. To the right you can add what interval of residues too superpose too
plus the chain id . (e.g: 1 100 A ).
B-factors
Add the B-factor crystal vibrations to give a estimate of the rigidity of the protein.
The initial minimization ticker
Forcefields can relax crystral structures so it reduces its energy. This can be ticked to relax the crystal structure before processing.
Some inconveniences
Currently you can make a full protein cycle morph. E.g: A to B to A. But if you do something like A to B to A to C then the first step will be overwritten due to the file name is the same.
This can be avoided by renaming the file even though it contains the same protein. Checking for file duplicate names is a lot of work for something which is rarely asked for. Though again if you want this implemented send me a mail (201304179@post.au.dk).
Finally the acceleration text field is strict, do not be creative like writting 1,15,0.4 or A-15,0.3 the program will default it to no acceleration value. Write in standard format.
Can i download an offline version
Currently, no. I am going to make an offline version which can be downloaded before this summer. Generally I am just a MSc. student at Aarhus university and i built
this program in just 5 weeks and I will have to finish a report in 2-3 weeks, so as you might expect my priority is to remove bugs before adding more off them..
Will new features be added?
Yes over time. I am as previousely stated going to make an offline version and a online film maker later on in my studies. I keep finding new smart ways
to get things done fast and simple but if you have any suggestions just send a mail to 201304179@post.au.dk. I will as a rule deny any suggestions which involve extensive computational power. This defeats the purpose of Morphinator as a fast program
Presentation: The Morphinator quick start guide
What will you get?
You will receive a multistage PDB file which can be viewed as a trajectory in the embeddded NGL viewer on this page. In addition you can download the multistage PDB file and every step.
The files can be further processed in rendering programs to make films. Though later on we will offer a simple online movie maker derived from NGL viewer. You can add B-fac visualization
as vibrations to the structure.
The principle idea behind Morphinator
The principle idea behind old school morphs was to linearly transform the protein atoms from A to B. Usually A and B are crystal structures and the intermediates are 'fictive steps'.
From these number of intermediates a quick film can be produced to visualize the protein dynamic behaviour of the protein.
The linear transformations were problematic as we would introduce steric clashes resulting in impossible energy requirements at room temperature.
In other words the produced films were highly unrealistic. Jesper Karlsen improved this by adding a geometric minimization through the phenix module for each step. This meant that the
transformation satisfied some basic constraints. The basic assumption in Morphinator is thus that any trajectory which transforms the protein from A to B will take the shortest possible path
satisfying forcefield constraints. This is obviousely not the entire truth as people who have professsions molecular dynamics would know, though as we will demonstrate in our article
the assumption imitates closely the real behaviour of the protein.
Creating your first morph film
The first thing you do is press "Add PDB to sequence.". You will now see a textfield has been added. In the textfield called "start PDB" we will add the name of the pdb
file you morph from (try 9b3b) and the PDB file text field you add the PDB to morph to(try 9b3r). The pdb files will be downloaded from the pdb database. If you have a custom
made PDB file you simple upload it and its name will appear in the txt field. You can manually type the name into the textfield of your uploaded pdb file
but be carefull it must have exact file name(name + extension e.g "Mypdb.pdb"). Morphinator also accepts .cif files. The "Steps" textbox you type the number of steps
to transform from A to B. Generally the more steps the smoother. Normally we recommend 20 steps.
Now you simple write the name of the results file plus the file extension: .pdb. Currently morphinator can only produce .pdb files. Press submit and you will
be taken to the next page after processing (usually takes 1-5 min.). This page tells you what residues have been moved as A and B must have same residues, all the wise residues will "magically" appear and dissapear
in the film. If you are satisfied press submit and the log box will monitor the progress and report back to you. Once complete a download buttom will appear or you can press "view with NGL" view
to watch the film in your browser.
Optional fields and good to know
The optional txt fields are blue. The tick boxes are ofcourse also optional.
The Model textfield
If you have a multistage PDB file, usually due to the data is collected from an NMR then you can select which PDB model you wish to use. If you do not select a model then
default is Model 0.
Delete field and upload file
You are required to delete the field with "delete field" buttom if left unused. We decided to add the upload buttom since people could potentially customely add ligands and see the
ligands move around the morph animation which was not originally in the PDB file. In addition if the PDB file is unpublished then it does not exists in the PDB databank.
Crop to previous tickbox
If you have a large PDB sequence of e.g. 12 steps and you want ligands to spawn and vanish from the PDB file then the tickbox is worthwhile. If left checked then imagine
a sequence A, B and C. Then we check C, it will only crop out residues which are not present in B, pr. default it will also crop out residues not in A.
Acceleration value
Due to morphinator has no time dimension you can put the number of steps proportional to each other to illustrate the rates for each step. Unfortunately the coordinate transformation
is linear. By addind the Acceleration value we can speed the transformation up or down over the morph. If < 1 then the transformation starts at a fast pace and slows down and if 1 <
it starts slow but speeds up. If i only want this to happend for an arbitary amount of steps (say we have 20 steps all together) then write 1-10,0.9,11-20,1.... (1-10 are the steps), 0.9
is the acceleration factor and 11-20 is the remaining steps and 1, is the default value indicating no acceleration happends what so ever.
Superpose to
This mostly allways has to be done in either Morphinator or in an external program. Often the proteins are in two unique coordinate systems so they must be aligned. You can
superpose to a PDB file in the morph seqeunce or something else from the protein databank or upload your own PDB file. To the right you can add what interval of residues too superpose too
plus the chain id . (e.g: 1 100 A ).
B-factors
Add the B-factor crystal vibrations to give a estimate of the rigidity of the protein.
The initial minimization ticker
Forcefields can relax crystral structures so it reduces its energy. This can be ticked to relax the crystal structure before processing.
Some inconveniences
Currently you can make a full protein cycle morph. E.g: A to B to A. But if you do something like A to B to A to C then the first step will be overwritten due to the file name is the same.
This can be avoided by renaming the file even though it contains the same protein. Checking for file duplicate names is a lot of work for something which is rarely asked for. Though again if you want this implemented send me a mail (201304179@post.au.dk).
Finally the acceleration text field is strict, do not be creative like writting 1,15,0.4 or A-15,0.3 the program will default it to no acceleration value. Write in standard format.
Can i download an offline version
Currently, no. I am going to make an offline version which can be downloaded before this summer. Generally I am just a MSc. student at Aarhus university and i built
this program in just 5 weeks and I will have to finish a report in 2-3 weeks, so as you might expect my priority is to remove bugs before adding more off them..
Will new features be added?
Yes over time. I am as previousely stated going to make an offline version and a online film maker later on in my studies. I keep finding new smart ways
to get things done fast and simple but if you have any suggestions just send a mail to 201304179@post.au.dk. I will as a rule deny any suggestions which involve extensive computational power. This defeats the purpose of Morphinator as a fast program
What will you get?
You will receive a multistage PDB file which can be viewed as a trajectory in the embeddded NGL viewer on this page. In addition you can download the multistage PDB file and every step. The files can be further processed in rendering programs to make films. Though later on we will offer a simple online movie maker derived from NGL viewer. You can add B-fac visualization as vibrations to the structure.The principle idea behind Morphinator
The principle idea behind old school morphs was to linearly transform the protein atoms from A to B. Usually A and B are crystal structures and the intermediates are 'fictive steps'. From these number of intermediates a quick film can be produced to visualize the protein dynamic behaviour of the protein. The linear transformations were problematic as we would introduce steric clashes resulting in impossible energy requirements at room temperature. In other words the produced films were highly unrealistic. Jesper Karlsen improved this by adding a geometric minimization through the phenix module for each step. This meant that the transformation satisfied some basic constraints. The basic assumption in Morphinator is thus that any trajectory which transforms the protein from A to B will take the shortest possible path satisfying forcefield constraints. This is obviousely not the entire truth as people who have professsions molecular dynamics would know, though as we will demonstrate in our article the assumption imitates closely the real behaviour of the protein.Creating your first morph film
The first thing you do is press "Add PDB to sequence.". You will now see a textfield has been added. In the textfield called "start PDB" we will add the name of the pdb file you morph from (try 9b3b) and the PDB file text field you add the PDB to morph to(try 9b3r). The pdb files will be downloaded from the pdb database. If you have a custom made PDB file you simple upload it and its name will appear in the txt field. You can manually type the name into the textfield of your uploaded pdb file but be carefull it must have exact file name(name + extension e.g "Mypdb.pdb"). Morphinator also accepts .cif files. The "Steps" textbox you type the number of steps to transform from A to B. Generally the more steps the smoother. Normally we recommend 20 steps. Now you simple write the name of the results file plus the file extension: .pdb. Currently morphinator can only produce .pdb files. Press submit and you will be taken to the next page after processing (usually takes 1-5 min.). This page tells you what residues have been moved as A and B must have same residues, all the wise residues will "magically" appear and dissapear in the film. If you are satisfied press submit and the log box will monitor the progress and report back to you. Once complete a download buttom will appear or you can press "view with NGL" view to watch the film in your browser.Optional fields and good to know
The optional txt fields are blue. The tick boxes are ofcourse also optional.The Model textfield
If you have a multistage PDB file, usually due to the data is collected from an NMR then you can select which PDB model you wish to use. If you do not select a model then default is Model 0.Delete field and upload file
You are required to delete the field with "delete field" buttom if left unused. We decided to add the upload buttom since people could potentially customely add ligands and see the ligands move around the morph animation which was not originally in the PDB file. In addition if the PDB file is unpublished then it does not exists in the PDB databank.Crop to previous tickbox
If you have a large PDB sequence of e.g. 12 steps and you want ligands to spawn and vanish from the PDB file then the tickbox is worthwhile. If left checked then imagine a sequence A, B and C. Then we check C, it will only crop out residues which are not present in B, pr. default it will also crop out residues not in A.Acceleration value
Due to morphinator has no time dimension you can put the number of steps proportional to each other to illustrate the rates for each step. Unfortunately the coordinate transformation is linear. By addind the Acceleration value we can speed the transformation up or down over the morph. If < 1 then the transformation starts at a fast pace and slows down and if 1 < it starts slow but speeds up. If i only want this to happend for an arbitary amount of steps (say we have 20 steps all together) then write 1-10,0.9,11-20,1.... (1-10 are the steps), 0.9 is the acceleration factor and 11-20 is the remaining steps and 1, is the default value indicating no acceleration happends what so ever.
Superpose to
This mostly allways has to be done in either Morphinator or in an external program. Often the proteins are in two unique coordinate systems so they must be aligned. You can superpose to a PDB file in the morph seqeunce or something else from the protein databank or upload your own PDB file. To the right you can add what interval of residues too superpose too plus the chain id . (e.g: 1 100 A ).
B-factors
Add the B-factor crystal vibrations to give a estimate of the rigidity of the protein.The initial minimization ticker
Forcefields can relax crystral structures so it reduces its energy. This can be ticked to relax the crystal structure before processing.
Some inconveniences
Currently you can make a full protein cycle morph. E.g: A to B to A. But if you do something like A to B to A to C then the first step will be overwritten due to the file name is the same. This can be avoided by renaming the file even though it contains the same protein. Checking for file duplicate names is a lot of work for something which is rarely asked for. Though again if you want this implemented send me a mail (201304179@post.au.dk). Finally the acceleration text field is strict, do not be creative like writting 1,15,0.4 or A-15,0.3 the program will default it to no acceleration value. Write in standard format.Can i download an offline version
Currently, no. I am going to make an offline version which can be downloaded before this summer. Generally I am just a MSc. student at Aarhus university and i built this program in just 5 weeks and I will have to finish a report in 2-3 weeks, so as you might expect my priority is to remove bugs before adding more off them..Will new features be added?
Yes over time. I am as previousely stated going to make an offline version and a online film maker later on in my studies. I keep finding new smart ways to get things done fast and simple but if you have any suggestions just send a mail to 201304179@post.au.dk. I will as a rule deny any suggestions which involve extensive computational power. This defeats the purpose of Morphinator as a fast program