Re: [COOT] Macros in COOT--use VB to write python code
Dear Andrew, Since I don't have the time to learn python fully and because there is not too many of examples of python scripting available for Coot, thus I use my expertise of VB to help me write the correct syntax for python script. then paste it into notepad and run it as a python script from Coot's GUI. For example I will paste an amino acid sequence of homologous proteins from ClustalW into an excel spreadsheet, then using VB to write a program that will put each amino acid into it's own spreadsheet cell as separate objects with some fancy colors ( as color codes) to make it pretty. Now, I can do all sorts of analyses of these sequences, like find the ones that are non-homologous between two proteins, put them in a table, let VB write the python syntax for "goto" and "mutate_autofit " of all these specific amino acids, paste it into notepad and "wala !" i have automation. That is ,I can goto (thus observe visually the mutational changes for oddballs) and mutate_autofit about 300 amino acids in about 10 min, rather than spending hours doing it manually. Wes In a message dated 1/19/2010 10:56:53 A.M. Central Standard Time, and...@mrc-lmb.cam.ac.uk writes: Having worked with O for many years I am only now getting serious with COOT. There are a couple of things that I would like to do that don't seem to be available (as far as I can tell), but which may well be possible using Macros. Unfortunately a quick Google has not revealed anything about how to use macros in COOT, but a colleague suggested they need to be written in Python or another language that I had not heard of before. So my first question is where can I find a low level description of how to write macros with some examples (I know nothing about Python, except that it is fashionable) ? There are specifically two things I want to be able to do: 1. Do an LSQ superposition using specified residues in multiple chains (superposing one oligomer on another). 2. To do a LSQ superposition of a homologous structure onto my working structure using +/- N residues about the current position, where N is a variable (not essential, could be fixed) and the current position is the last residue that I clicked on. Thanks Andrew
Re: [COOT] Macros in COOT--use VB to write python code
Goodness, sounds like fun. Coot does have an align&mutate function of course, but you don't get to fiddle with the sequence alignment - Coot uses its own alignment [1]. My understanding is that should be fine for ~70% sequence identity or better. My feeling though is that it is not widely used. So my question to the community is: Is there a need to be able to use an alignment rather than simply a target sequence? Thanks, Paul. [1] courtesy of mmdb Wes Ozarowski wrote: Dear Andrew, Since I don't have the time to learn python fully and because there is not too many of examples of python scripting available for Coot, thus I use my expertise of VB to help me write the correct syntax for python script. then paste it into notepad and run it as a python script from Coot's GUI. For example I will paste an amino acid sequence of homologous proteins from ClustalW into an excel spreadsheet, then using VB to write a program that will put each amino acid into it's own spreadsheet cell as separate objects with some fancy colors ( as color codes) to make it pretty. Now, I can do all sorts of analyses of these sequences, like find the ones that are non-homologous between two proteins, put them in a table, let VB write the python syntax for "goto" and "mutate_autofit " of all these specific amino acids, paste it into notepad and "wala !" i have automation. That is ,I can goto (thus observe visually the mutational changes for oddballs) and mutate_autofit about 300 amino acids in about 10 min, rather than spending hours doing it manually. Wes In a message dated 1/19/2010 10:56:53 A.M. Central Standard Time, and...@mrc-lmb.cam.ac.uk writes: Having worked with O for many years I am only now getting serious with COOT. There are a couple of things that I would like to do that don't seem to be available (as far as I can tell), but which may well be possible using Macros. Unfortunately a quick Google has not revealed anything about how to use macros in COOT, but a colleague suggested they need to be written in Python or another language that I had not heard of before. So my first question is where can I find a low level description of how to write macros with some examples (I know nothing about Python, except that it is fashionable) ? There are specifically two things I want to be able to do: 1. Do an LSQ superposition using specified residues in multiple chains (superposing one oligomer on another). 2. To do a LSQ superposition of a homologous structure onto my working structure using +/- N residues about the current position, where N is a variable (not essential, could be fixed) and the current position is the last residue that I clicked on. Thanks Andrew
Re: [COOT] Macros in COOT--use VB to write python code
Is my understanding correct that what Wes describes can be accomplished in the following three steps: 1. Apply CHAINSAW using sequence alignment 2. fill-partial-residues 3. fit-protein (optional) Seems to me that moving chainsaw step into coot will not save much time (if at all). Cheers, Ed. On Thu, 2010-01-28 at 10:10 +, Paul Emsley wrote: > Goodness, sounds like fun. > > Coot does have an align&mutate function of course, but you don't get to > fiddle with the sequence alignment - Coot uses its own alignment [1]. > My understanding is that should be fine for ~70% sequence identity or > better. My feeling though is that it is not widely used. So my question > to the community is: Is there a need to be able to use an alignment > rather than simply a target sequence? > > Thanks, > > Paul. > > [1] courtesy of mmdb > > > Wes Ozarowski wrote: > > > > Dear Andrew, > > > > Since I don't have the time to learn python fully and because > > there is not too many of examples of python scripting available for > > Coot, thus I use my expertise of VB to help me write the correct > > syntax for python script. then paste it into notepad and run it as a > > python script from Coot's GUI. > > > > For example I will paste an amino acid sequence of homologous > > proteins from ClustalW into an excel spreadsheet, then using VB to > > write a program that will put each amino acid into it's own > > spreadsheet cell as separate objects with some fancy colors ( as color > > codes) to make it pretty. Now, I can do all sorts of analyses of these > > sequences, like find the ones that are non-homologous between two > > proteins, put them in a table, let VB write the python syntax for > > "goto" and "mutate_autofit " of all these specific amino acids, paste > > it into notepad and "wala !" i have automation. That is ,I can goto > > (thus observe visually the mutational changes for oddballs) and > > mutate_autofit about 300 amino acids in about 10 min, rather than > > spending hours doing it manually. > > > >Wes > > > > > > > > > > > > > > In a message dated 1/19/2010 10:56:53 A.M. Central Standard Time, > > and...@mrc-lmb.cam.ac.uk writes: > > > > Having worked with O for many years I am only now getting serious > > with > > COOT. There are a couple of things that I would like to do that > > don't > > seem to be available (as far as I can tell), but which may well be > > possible using Macros. > > > > Unfortunately a quick Google has not revealed anything about how to > > use macros in COOT, but a colleague suggested they need to be > > written > > in Python or another language that I had not heard of before. > > > > So my first question is where can I find a low level description of > > how to write macros with some examples (I know nothing about Python, > > except that it is fashionable) ? > > > > There are specifically two things I want to be able to do: > > > > 1. Do an LSQ superposition using specified residues in multiple > > chains > > (superposing one oligomer on another). > > > > 2. To do a LSQ superposition of a homologous structure onto my > > working > > structure using +/- N residues about the current position, where N > > is > > a variable (not essential, could be fixed) and the current > > position is > > the last residue that I clicked on. > > > > Thanks > > > > Andrew > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
