Re: [ccp4bb] Topology diagram
Dear community, Thanks for your helpful answers. @Xavier: Obviously, I knew TopDraw, but as mentioned by Andy “TOPDRAW doesn't interpret a pdb file, it just allows you to draw your own topology diagram.” And I wanted it to be as simple as possible for my biochemist colleague with no access to ccp4 programs. @Andy: The link to generate a PDBsum output, without installing the program, is: https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html @Deborah: Thanks for the link of Overprot (https://overprot.ncbr.muni.cz/) @Tom: Pro-origami was exactly what I was looking for, unfortunately the web server is gone (what a pity). Many thanks for the link to actually install the program: (https://sites.google.com/site/alexdstivala/home/pro-origami), which would be extremely useful. Always a pleasure to read and get useful answers from ccp4db, Bests, Lionel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Topology diagram
Dear Lionel, If you want a programme that takes a PDB file and automatically generates a topology diagram, then Pro-origami may be the software you need (https://sites.google.com/site/alexdstivala/home/pro-origami) - it generates prettier diagrams than PDBsum, and the diagrams are output as .svg files which can be edited in Illustrator to add custom labelling and so on. Best, Tom On 30 May 2024, at 16:32, Lionel wrote: External Sender: Use caution. Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I believe is a “key notation” topology diagram. It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and I would say (without offence) a bit ugly. After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found nothing helpful. It seems that “old” tools like pro-origami are gone/unavailable. I would greatly appreciate any advice on possible website or more specialized program (even if I would do the “webserver” task myself). Best, Lionel To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7C%7Cec3a11ec199f4e4ff6a208dc80bdd509%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638526800036635794%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=6RsqWYBGsoo6%2BlCLUPr0OY3TY0WyFCJwNlRyNtI2jZ4%3D&reserved=0 This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7C%7Cec3a11ec199f4e4ff6a208dc80bdd509%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638526800036645701%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=eWDNnowlcNl7bPUz9%2FddEiiv9oseBPiYiNRnmecUHdg%3D&reserved=0, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7C%7Cec3a11ec199f4e4ff6a208dc80bdd509%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638526800036650409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=6YBuWT%2F1OSpMTLa%2FppeUWwKcWUg7at7CV%2FF4ifnecOs%3D&reserved=0, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7C%7Cec3a11ec199f4e4ff6a208dc80bdd509%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638526800036654347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=gO37KLqO%2Fv2Fvn%2FozKqwVHfL5Xvt2U1Ffve%2Fx5q9MmY%3D&reserved=0 The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Topology diagram
Dear Lionel, I would say it depends what do you intend to use the topology diagram for? I personally like Overprot (https://overprot.ncbr.muni.cz/) as you can also see topological diagram for the CATH protein family. Kind regards, Deborah On 30/05/2024 16:32, Lionel wrote: Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I believe is a “key notation” topology diagram. It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and I would say (without offence) a bit ugly. After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found nothing helpful. It seems that “old” tools like pro-origami are gone/unavailable. I would greatly appreciate any advice on possible website or more specialized program (even if I would do the “webserver” task myself). Best, Lionel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- --- Deborah Harrus, Ph.D. PDBe Archive Project Leader, Biocuration Lead PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK http://www.PDBe.org --- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Topology diagram
Dear Lionel and Xavier, Unfortunately TOPDRAW doesn't interpret a pdb file, it just allows you to draw your own topology diagram. PDBSUM (available from https://www.ebi.ac.uk/thornton-srv/software/PDBsum1/) has a topology diagram as part of the output. You can also access a database of released structures here: https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ and there is a link to the Generate webpage there allows you to securely upload a pdb file if you don't wish to install the software yourself. Hope this helps, Andy Purkiss From: CCP4 bulletin board on behalf of Xavier Brazzolotto Sent: 30 May 2024 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Topology diagram External Sender: Use caution. My Google search led directly to <https://www.ccp4.ac.uk/html/topdraw.html> TOPDRAW (CCP4: Supported Program) — CCP4 documentation<https://www.ccp4.ac.uk/html/topdraw.html> ccp4.ac.uk<https://www.ccp4.ac.uk/html/topdraw.html> [favicon.ico]<https://www.ccp4.ac.uk/html/topdraw.html> HTH Le 30 mai 2024 à 17:32, Lionel a écrit : Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I believe is a “key notation” topology diagram. It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and I would say (without offence) a bit ugly. After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found nothing helpful. It seems that “old” tools like pro-origami are gone/unavailable. I would greatly appreciate any advice on possible website or more specialized program (even if I would do the “webserver” task myself). Best, Lionel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Topology diagram
My Google search led directly to https://www.ccp4.ac.uk/html/topdraw.html HTH > Le 30 mai 2024 à 17:32, Lionel a écrit : > > Dear community, > > A biochemist asks me if I knew a webserver/tool to draw topology diagram of > protein from a deposited pdb or part of it, ideally allowing edition (label, > colour, etc...). > > For a better understanding, the topology diagram’s representation is as the > picture attached, which I believe is a “key notation” topology diagram. > > It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) > and I would say (without offence) a bit ugly. > > After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found > nothing helpful. > It seems that “old” tools like pro-origami are gone/unavailable. > > I would greatly appreciate any advice on possible website or more specialized > program (even if I would do the “webserver” task myself). > > Best, > Lionel > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Topology diagram
Dear community, A biochemist asks me if I knew a webserver/tool to draw topology diagram of protein from a deposited pdb or part of it, ideally allowing edition (label, colour, etc...). For a better understanding, the topology diagram’s representation is as the picture attached, which I believe is a “key notation” topology diagram. It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and I would say (without offence) a bit ugly. After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found nothing helpful. It seems that “old” tools like pro-origami are gone/unavailable. I would greatly appreciate any advice on possible website or more specialized program (even if I would do the “webserver” task myself). Best, Lionel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] AW: [ccp4bb] topology diagram
Hi Neeraj, Try pdbsum. looks nice for mine. You can upload your structure there... http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/upload.html hth... gregor -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Neeraj Gesendet: Mittwoch, 11. Juni 2008 17:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] topology diagram Hi all, wondering if anyone knows of a user friendly and esy to use program for generating topology diagrams for proteins. Any help would be very useful to me. thanks, Neeraj -- Neeraj Kapoor TPCB Graduate Fellow Sakmar Lab/ Molecular Biology & Biochemistry The Rockefeller University 1230 York Avenue, RRB 510 New York, NY 10021 lab.1.212.327.8284:fax.7904 mobile: 917.535.2030 http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html
Re: [ccp4bb] topology diagram
Hi Neeraj, CCP4 has a program which allows one to draw topology diagram manually...it's easy to learn and use. http://stein.bioch.dundee.ac.uk/~charlie/software/topdraw/ There is another program called "TOPS" (website is currently under maintenance) which generates topology diagram according to your pdb file. http://www.tops.leeds.ac.uk/ Hope it helps! Simanshu On Wed, Jun 11, 2008 at 11:07 AM, Neeraj <[EMAIL PROTECTED]> wrote: > Hi all, > wondering if anyone knows of a user friendly and esy to use program for > generating topology diagrams for proteins. Any help would be very useful to > me. > > thanks, > Neeraj > > -- > Neeraj Kapoor > TPCB Graduate Fellow > Sakmar Lab/ Molecular Biology & Biochemistry > The Rockefeller University > 1230 York Avenue, RRB 510 > New York, NY 10021 > lab.1.212.327.8284:fax.7904 > mobile: 917.535.2030 > http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html > -- Dhirendra K Simanshu Research Fellow Memorial Sloan-Kettering Cancer Center New York, NY, USA
[ccp4bb] topology diagram
Hi all, wondering if anyone knows of a user friendly and esy to use program for generating topology diagrams for proteins. Any help would be very useful to me. thanks, Neeraj -- Neeraj Kapoor TPCB Graduate Fellow Sakmar Lab/ Molecular Biology & Biochemistry The Rockefeller University 1230 York Avenue, RRB 510 New York, NY 10021 lab.1.212.327.8284:fax.7904 mobile: 917.535.2030 http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html
