Re: [ccp4bb] X-PLOR

Nadir, There is an explicit bulletin board for questions regarding CNS and XPLOR. I would suggest posting your question there. http://tech.dir.groups.yahoo.com/group/cnsbb/ Cheers, Francisco -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

[ccp4bb] Calculating ED Maps from structure factor files with no sigma

Hello everyone, My apologies if this comes as basic, but I wanted to get the expert's take on whether or not the sigmaF values are required in the calculation of an electron density map. If I look at the standard ED equation, sigma's don't appear to be a requirement but all the scripts that

Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma

/pdb_redo/hf/1hfs/index.html) was indeed a great resource and I'm certain to use it again. Thanks! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Francisco Hernandez-Guzman Sent: Tuesday, May 22, 2012 9:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculating ED Maps from

Re: [ccp4bb] DNA/RNA modeling

Hi Jens, You can try the free DS Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php It comes with a free molecular builder for proteins, dna/rna and ligands. Please note that if you do need to make anything more interesting (energy calculations,

Re: [ccp4bb] Protein-Protein Interactions

Hi Lorenzo, If the structure for your receptor is unknown, then you can use Homology Modeling methods to get a rough idea of the structure, MODELLER is a well know tool for this (http://salilab.org/modeller/). Of course depending on your % similarity to the template, the higher the %

Re: [ccp4bb] Protein volume

Hi Theresa, You can use our free Discovery Studio Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php You can select the region of choice (in your case the transmembrane domain) and create a surface around it (Structure - Surface - Add). Then in the Molecular

Re: [ccp4bb] Improving Homology Models

commercial suite Discovery Studiohttp://accelrys.com/products/discovery-studio/, but you can also access them directly from their respective labs. Kind regards, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager Accelrys Software, Inc. From: CCP4 bulletin board [mailto:CCP4BB

Re: [ccp4bb] How to compare B-factors between structures?

Hi Yarrow, I'm sure other visualizing tools can do this, but I just wanted to share that our free Discovery Studio Visualizerhttp://accelrys.com/products/discovery-studio/visualization-download.php can do this quite easily. Contact me off the list and we can set up a time when I can show

Re: [ccp4bb] [off-topic] CNS solve profit license

Hi Genie, I'll ask someone from our Korea office to get in touch with you regarding your request. CNS for profit licenses do have to be licensed through Accelrys. Thanks, Francisco Francisco Hernandez-Guzman, PhD Sr. Product Manager Accelrys Software, Inc From: CCP4 bulletin board

Re: [ccp4bb] delete subject

Hi all, This has indeed been a highly informative and educational thread from many view points, and it highlights the opportunities and challenges that scientists face today by having access to tools like the CCP4BB . I just wanted to touch on something that was briefly alluded to at the early

Re: [ccp4bb] off-topic: Discovery Studio software

- Protein reports - and much more... Many of the features that were previously available in the paid version, are now offered for free with this new version. I encourage everyone to give it a try. Thanks, Francisco Francisco Hernandez-Guzman Product Manager Accelrys, San Diego, CA

Re: [ccp4bb] Off-topic: ELNs

Hi Seiji, A nice web base solution is the iLabber from Contur. It has been a popular option for many academic labs around the globe. http://www.contur.com/home/ Cheers, Francisco Sr. Product Manager Accelrys, Inc. -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment

can select your own custom coloring for each property. I have attached a small screenshot of the view for your sample picture trying to match your coloring scheme. Cheers, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager http://accelrys.com From: CCP4 bulletin board

Re: [ccp4bb] On pKa of Aspartic acid

Hi Deepak, With regards observed pKa shifts, Prof. Ondrechen from Northeastern University has had a long interest in this field. http://www.northeastern.edu/org/wp/ Under the computational tools that she has developed a program called THEMATICS that allows you to predict the pka of titratable