[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] Problem in running ARP_WARP in CCP4i...solved....
Dear All, The problem is solved by updating the tcsh version from 6.14.00 to 6.14.17. Thanks to Santosh, Ioan and Lamzin. With regards S. Karthikeyan On 3/7/2013 7:55 PM, Ioan Vancea wrote: Dear Karthikeyan, In order to trace the error may I ask you, please, to change the first line in auto_tracing.sh by adding -x as option to csh: #!/bin/csh -xf and then rerun the command to see where it stops. Cheers, Ioan P.S. I remember that I have seen that kind of error (for shell scripts in general) when the linux PATH/command length is too long. On Mar 7, 2013, at 2:38 PM, S. Karthikeyan wrote: Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Tel: +49 (0)40 89902-205 Email: ivan...@embl-hamburg.de __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
Re: [ccp4bb] Off-topic: Fungal growth in robot trays
We add 0.02% Azide to all the water used for washing in our Phoenix, and that seems to help. Janet Newman Principal Scientist / Director, Collaborative Crystallisation Centre CSIRO Material Science and Engineering 343 Royal Parade Parkville. VIC. 3052 Australia Tel +613 9662 7326 Email janet.new...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Viswanathan Chandrasekaran [v...@biochem.utah.edu] Sent: 09 March 2013 10:24 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Fungal growth in robot trays Dear All: I would like some advice on getting rid of persistent fungal growth in 96-well sitting drop crystal plates that were set up using a Phoenix robot. 24-well sitting drop trays prepared by hand don’t have this problem. Washing the robot with 0.5% bleach followed by plenty of water had no effect. Is adding sodium azide directly to commercial screen hotels (or the protein sample) a good idea? If so, how much should I add? Other suggestions are welcome. I will post a summary of all replies. Thank you. Best, Vish
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
