Re: [ccp4bb] Refmac dictionary

Hi My apologies. This is indeed a silly question. It appears I forgot to remove the extra O when linking them together! Sam On Wed, 3 Apr 2019 at 07:21, Sam Tang wrote: > Dear all > > Hello again. > > We have another protein-RNA dataset which we are trying to refine. For > this dataset we hav

[ccp4bb] Refmac dictionary

Dear all Hello again. We have another protein-RNA dataset which we are trying to refine. For this dataset we have three OMU nucleotides modelled. We got the monomer from Coot 'Get Monomer'. Refmac returned the following error: ERROR : atom :OP3 OMU 2 CCC is absent in the librar

Re: [ccp4bb] installation of XDS

Hi Nadine, it sounds like you downloaded the tar-file that has the documentation, instead of the tar-file that has the binaries. You want to download ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz , and un-tar the file at /home/Programs - this will overwrite your

[ccp4bb] Research Technician Position in Chromatin Biology

A research technician position is available in the laboratory of Dr. Karim-Jean Armache, Assistant Professor in the Structural Biology Program at the Skirball Institute of Biomedical Research—NYU Medical Center, New York, USA. We are looking for creative individuals with a strong interest in prot

Re: [ccp4bb] beryllium chloride

The older fellows might well remember the huge Be windows on the ADSC multi-wire detectors – miraculously we survived them simply by common sense dictating (i) don’t eat it, (ii) don’t breathe it, and (iii) don’t rub your nose in it…. Cheers, BR From: CCP4 bulletin board On Behal

Re: [ccp4bb] beryllium chloride

There are plenty of heavy metals that have little to no physiological significance, because biomes evolved in their absence. But beryllium is interesting because it’s so light and nonabundant in comparison to related elements like Li or Mg. So since mammals never evolved with free Be2+ around,

Re: [ccp4bb] unidentified crescent-shaped electron density

Has anyone ever done the experiment of switching precipitants/cryoprotectants and verifying that this crown-of-PEG around lysine goes away when you do? Just curious, -James Holton MAD Scientist On 4/1/2019 4:26 PM, Paul Emsley wrote: Agreed. "PG4" - so that you don't have to go searching for

Re: [ccp4bb] beryllium chloride

I remember from biochemistry class that it’s the one element that has no known physiological role—is that still true? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (5

Re: [ccp4bb] beryllium chloride

The lung disease is called berylliosis and is an allergic-type response that leads to fibrosis in the lungs. A significant percentage of the population has allergic reactions to beryllium, but there is no very accurate method for prescreening this; I read somewhere even lung biopsies are only ab

Re: [ccp4bb] installation of XDS

Hi Nadine The program is probably correct - I suspect you have no XDS.INP in there I recommend using e.g. generate_XDS.INP for this purpose https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP You may find the wider XDS wiki worth a read Best wishes Graeme On 2 Apr 20

[ccp4bb] installation of XDS

Hello, I need help installing XDS on the computer. Apparently the current lisence expired on March 31 2019, which is why I downloaded and extracted the XDS_html_doc.tar.gz from http://xds.mpimf-heidelberg.mpg.de/html_doc/downl

Re: [ccp4bb] beryllium chloride

Sometime ago when I was watching a Youtube video on magnetron I learnt that at least at at certain point of time the antenna port of the magnetron was sealed using beryllium oxide ceramic(probably for its high thermal conductivity). The video maker warned that this ceramic was extremely dangerou

Re: [ccp4bb] modelling of modified RNA

On 02/04/2019 14:28, Sam Tang wrote: Hello Hello. I have been refining a protein-RNA complex with Refmac. The RNA we used was tagged with a Cy label. I modelled the RNA in Coot using the RCrane add-on and manually built the Cy tag. However after Refmac (also via Coot) the linkage between C

[ccp4bb] PhD/ postdoc positions on studies on the life cycle and applications of virophages: Max Planck Institute, Heidelberg, Germany

Ph.D. and Postdoctoral positions dedicated to biophysical and spectroscopic/structural studies on the life cycle of virophages and their applications as nano-containers available in Jochen Reinstein's lab http://www.mpimf-heidelberg.mpg.de/14072516/gruppereinstein at the Max Planck Institute fo

[ccp4bb] modelling of modified RNA

Hello I have been refining a protein-RNA complex with Refmac. The RNA we used was tagged with a Cy label. I modelled the RNA in Coot using the RCrane add-on and manually built the Cy tag. However after Refmac (also via Coot) the linkage between Cy and the RNA was always broken. I guess I must hav

Re: [ccp4bb] beryllium chloride

Hi Bob, for something probably less toxic (but also less sweet tasting), try beryllium ortho-silicate (Be2SiO4). Crystals of sufficient purity serve as excellent test crystals, with low absorption and ridiculous diffraction. You might need a jeweler to cut them down to size. All best. Andreas

Re: [ccp4bb] beryllium chloride

Yes both soluble beryllium salts and powdered beryllium metal even applied to the skin are known to cause sensitization and is a route into the bloodstream where it is highly carcinogenic (I am not speaking from experience!). Yet strangely the one source of beryllium that many people (at least the

Re: [ccp4bb] beryllium chloride

1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 2. Bob, I studied that page, and couldn’t get past BeCl2 is known to have a “sweetish taste.” I’m very glad chemists no longer characterize chemicals by their taste anymore... -- Aaron Finke Staff Scien

[ccp4bb] Open position structural biology at University of Milan

Dear, here to advertise two postdoc positions in my lab at the Department of Biosciences, University of Milan, Italy. The scientific project will deal on structural biology (Cryo-EM and crystallography) and biophysics of protein aggregation and amyloid fibril formation. Specifically the projects

Re: [ccp4bb] unidentified crescent-shaped electron density

I have seen similar density with a fatty acid (C16 or C18). In our case the there was also a lysine side chain forming a salt bridge with the carboxylate. Furthermore, the pocket was very hydrophobic. What about this one? -Peer On 02.04.2019 03:12, Zhen Luo wrote: Hi everyone, Thank you ve