Re: [ccp4bb] Peptide solubility issues

Hello Mo Wong, Some points below are good, but don't underestimate custom peptides sometimes... can be much harder/expensive than recombinant proteins. If you ordered the peptides it is good to know how they synthesized them, and how the elution profiles during purification (RP HPLC..) looked

[ccp4bb] size of a flexible pdb structure

Dear all, sorry for asking an off topic question. My protein is composed of two domains connected by a flexible linker (15aa). after 50ns simulation i came across the fact that one domain is flexible. so my question is that how could i be able to calculate the size of molecule or radius of my

Re: [ccp4bb] size of a flexible pdb structure

Dear Rajan kumar choudhary, could you explain why you expect the volume to depend on the conformation of the molecule? Do you have some effective volume in mind, e.g. the elution volume during size exclusion chromatography? Regards, Tim On Wed, Mar 05, 2014 at 08:42:21PM +0530, rajan kumar

[ccp4bb] CCP4 lib file

Hi, I am trying to refine (Refmac5 on CCP4) a protein structure containing ligands that are exclusively glucose units but refinement fails because I don't have a lib file for the sugars. Can I get help on making lib files please? Thank you, Remie

Re: [ccp4bb] size of a flexible pdb structure

Hi rajan I guess calculating radius of gyration for your whole protein with time will tell you about the size variation at difeerent time points or you canm say different frames. This is how you can cluster your whole trajectory PDBs into a few clusters and then get the representative PDBs from

Re: [ccp4bb] CCP4 lib file

There are lots of GLUCOSE type lib files for different sugars. One way to find what is available is: From the REfinement GUI click Monomer library sketcher You get a window with File in the top LH corner Click on that and ask for Read monomer from library Then enter a key word GLUCOSE and you

[ccp4bb] Post-doctoral Fellowships at the University of Texas

Macromolecular Crystallography, Biophysics and Biochemistry A post-doctoral fellowship position is available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the

Re: [ccp4bb] size of a flexible pdb structure

Dear Rajan, Since you raised your question about calculating the radius of your molecule. here my suggestion, a bit long back I heard about the program HYDROPRO I am not sure its going to be work for you, but you may give a try. I think the program calculates the radius of gyration !  best wishes,

[ccp4bb] Off-Topic: Hydrodynamic/Thermodynamic Workshop in Dallas, TX

Dear All, I am very pleased to announce that a workshop entitled “Methods for the Analysis of Thermodynamic and Hydrodynamic Properties of Macromolecules and their Complexes” will be held on May 19-23, 2014 in Dallas, TX, at The University of Texas Southwestern Medical Center. I post here

[ccp4bb] Job opportunity at Constellation pharmaceuticals in Cambridge MA

Constellation Pharmaceuticals has the following job opportunity. Please use the 'care...@constellationpharma.com' email to reply. Scientist - Structural Biology Constellation Pharmaceuticals leverages insights from the rapidly expanding field of epigenetics to discover and develop small

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

A rather US-centric question on passive 3D monitors... I'm just getting set up in the US, and I'm surprised on how few passive 3D monitors seem to be around - many models seem listed as 'out of stock' when looking in the usual places (Amazon, NewEgg, BestBuys, Walmart etc.) The best deal I

Re: [ccp4bb] Peptide solubility issues

Many thanks to all the people who contacted me. I actually went rogue and decided to initially reconstitute in 10mM glycine, pH 9.5 to 2 mg/mL, sonicate for a few seconds and then immediately add an equal volume of more concentrated neutral pH buffer to minimize any possibility of alkaline

Re: [ccp4bb] Peptide solubility issues

For that purpose we’ve developed this expression system that may or may not be useful to your specific problem: http://www.ncbi.nlm.nih.gov/pubmed/23996492 J Mol Recognit.http://www.ncbi.nlm.nih.gov/pubmed/23996492# 2013 Oct;26(10):496-500. doi: 10.1002/jmr.2292. Development of a multifunctional

[ccp4bb] PhD position to explore the molecular mechanisms of ubiquitin signaling

Dear colleagues, We invite applications for a PhD position in the research group of Dr. Sonja Lorenz at the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg.The successful applicantwill have the opportunity to be part of the 'Graduate School of Life Sciences' in Würzburg-

[ccp4bb] Efforts been made to solve protein (soluble) aggregation

Dear CCP4 friends, I have been searching around the CCP4 mails for the discussion of soluble protein aggregations, as I have the same problem recently. Many efforts I have tried but without success. Here, I would like to summarise what I have done and maybe any of you come across some ideas. 1.