Re: [ccp4bb] how to make protein topology figure based on its structure
Dear All, I cannot resist responding to this request that Lisa has made. I am very surprised that no one has mentioned Roman Laskowski's program PDBSUM. It does a great job applying secondary structure prediction by Lisa Holme and will mark the beginning and ending of strands and helices. Try it. Michael James On Sat, Mar 9, 2013 at 1:02 PM, Edward A. Berry ber...@upstate.edu wrote: Still, I would second Lisa's question. Your google search gives a lot of false hits, and one doesn't want to download and install a dozen programs (with license forms to fill out in some cases) to see which one works, when Partha can tell us that Pro-origami will do it and provide a link to the description. Seems to be just what I've been looking for. Thanks, Partha! Anastassis Perrakis wrote: On 9 Mar 2013, at 12:11, Jon Agirre wrote: Espript will do. http://espript.ibcp.fr Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I could not resist pasting your question to google - its a good thing to do before pasting the question in your email client - it can give you a strange sense of satisfaction and us (or at least me) less Saturday morning fun. http://lmgtfy.com/?q=%5Bccp4%**5D+how+to+make+protein+** topology+figure+based+on+its+**structurehttp://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure A. Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com mailto: science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
Re: [ccp4bb] how to make protein topology figure based on its structure
My point was that the second hit in the google list, was the CCP4's own program to make topology diagrams. There was no issue of installing anything - it was an issue of looking if ccp4 has a program that makes topology diagrams. If you don't like that program, you could ask is there another program other than ccp4's TopDraw to make topological diagrams?. Asking the ccp4bb without looking at the ccp4 list of software for what you are looking for, is - in my view - sloppy and shows lack of effort. Possibly I am too demanding. I should add, that if you type to google something like topology diagram protein structure you get lots of useful hits, including PDBSUM and Pro-Origami, in the first page. I do not want to discourage people asking question in the bb, but at the same time I think that some problem solving hierarchy of the order 'google it' - 'ask your lab-mates' - 'ask your boss' - 'mail 5,000 people' can save everybody lots of time, can help people to grow, and might even make the bb more fun. My two cents - and sorry for the long and likely unnecessary and redundant email. A. On Sat, Mar 9, 2013 at 1:02 PM, Edward A. Berry ber...@upstate.edu wrote: Still, I would second Lisa's question. Your google search gives a lot of false hits, and one doesn't want to download and install a dozen programs (with license forms to fill out in some cases) to see which one works, when Partha can tell us that Pro-origami will do it and provide a link to the description. Seems to be just what I've been looking for. Thanks, Partha! Anastassis Perrakis wrote: On 9 Mar 2013, at 12:11, Jon Agirre wrote: Espript will do. http://espript.ibcp.fr Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I could not resist pasting your question to google - its a good thing to do before pasting the question in your email client - it can give you a strange sense of satisfaction and us (or at least me) less Saturday morning fun. http://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure A. Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com mailto:science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
Re: [ccp4bb] how to make protein topology figure based on its structure
I like Topdraw very much, have been using it since 2005. But as far as i understand it will not make a topological figure of my protein with a b-sheet and helix based on its crystal structure. It is a drawing tool to help you make your own topology drawing. (I will be very happy to learn if I am wrong about that). The correct answer from my point of view is Pro-Origami, which did not show up in the first page of hits. I had a chance to play with it a little, and it does a very nice job of organizing beta sheets, for example with 1RIE. I would probably take its output as a starting point for making my own diagram with topdraw. It is not so useful with helices - a 4-helix bundle which I would draw as parallel up and down cylinders was drawn in a straight line one after the other - like chain C of 1ppj. So there are at least 3 things people mean by a protein topology program- one that defines the secondary structure, like espript, one that gives you drawing tools to make your own based on the output of those programs, like TopDraw, and one with artificial intelligence that automates the whole thing like ProOrigami. I am aware that the pdbsum website has nice topology drawings, didn't realize you could use it on your own undeposited structures. eab Anastassis Perrakis wrote: My point was that the second hit in the google list, was the CCP4's own program to make topology diagrams. There was no issue of installing anything - it was an issue of looking if ccp4 has a program that makes topology diagrams. If you don't like that program, you could ask is there another program other than ccp4's TopDraw to make topological diagrams?. Asking the ccp4bb without looking at the ccp4 list of software for what you are looking for, is - in my view - sloppy and shows lack of effort. Possibly I am too demanding. I should add, that if you type to google something like topology diagram protein structure you get lots of useful hits, including PDBSUM and Pro-Origami, in the first page. I do not want to discourage people asking question in the bb, but at the same time I think that some problem solving hierarchy of the order 'google it' - 'ask your lab-mates' - 'ask your boss' - 'mail 5,000 people' can save everybody lots of time, can help people to grow, and might even make the bb more fun. My two cents - and sorry for the long and likely unnecessary and redundant email. A. On Sat, Mar 9, 2013 at 1:02 PM, Edward A. Berry ber...@upstate.edu mailto:ber...@upstate.edu wrote: Still, I would second Lisa's question. Your google search gives a lot of false hits, and one doesn't want to download and install a dozen programs (with license forms to fill out in some cases) to see which one works, when Partha can tell us that Pro-origami will do it and provide a link to the description. Seems to be just what I've been looking for. Thanks, Partha! Anastassis Perrakis wrote: On 9 Mar 2013, at 12:11, Jon Agirre wrote: Espript will do. http://espript.ibcp.fr http://espript.ibcp.fr/ Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I could not resist pasting your question to google - its a good thing to do before pasting the question in your email client - it can give you a strange sense of satisfaction and us (or at least me) less Saturday morning fun. http://lmgtfy.com/?q=%5Bccp4%__5D+how+to+make+protein+__topology+figure+based+on+its+__structure http://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure A. Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com mailto:science...@gmail.com mailto:science...@gmail.com mailto:science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
[ccp4bb] how to make protein topology figure based on its structure
Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
Re: [ccp4bb] how to make protein topology figure based on its structure
Espript will do. http://espript.ibcp.fr/ Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
Re: [ccp4bb] how to make protein topology figure based on its structure
On 9 Mar 2013, at 12:11, Jon Agirre wrote: Espript will do. http://espript.ibcp.fr Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I could not resist pasting your question to google - its a good thing to do before pasting the question in your email client - it can give you a strange sense of satisfaction and us (or at least me) less Saturday morning fun. http://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure A. Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
Re: [ccp4bb] how to make protein topology figure based on its structure
Still, I would second Lisa's question. Your google search gives a lot of false hits, and one doesn't want to download and install a dozen programs (with license forms to fill out in some cases) to see which one works, when Partha can tell us that Pro-origami will do it and provide a link to the description. Seems to be just what I've been looking for. Thanks, Partha! Anastassis Perrakis wrote: On 9 Mar 2013, at 12:11, Jon Agirre wrote: Espript will do. http://espript.ibcp.fr Well, if you want a topology diagram, espipt will not do. Brilliant as it may be, it will annotate the topology linearly on top of a set of aligned sequences (and more!). As for a topology diagram, I could not resist pasting your question to google - its a good thing to do before pasting the question in your email client - it can give you a strange sense of satisfaction and us (or at least me) less Saturday morning fun. http://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure A. Good luck, Jon On 9 Mar 2013 11:52, LISA science...@gmail.com mailto:science...@gmail.com wrote: Hi all, I want to make a topological figure of my protein with a b-sheet and helix based on its crystal structure. Please recommend some online sever of software? Thank you. lisa
