Re: [ccp4bb] Incubator for crystallization

We use wine refrigerators. Peltier cooling, no compressor, no vibrations, cheap. They look nice too. But they can't cool to 4C. Aloha, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu

Re: [ccp4bb] workstation crystallography

The more recent integrated graphics chips, starting from the Intel HD3000, have adequate performance for crystallography. Really, most crystallography applications are less computationally demanding than video games now. I think the most important issue is to make sure your hardware plays nicely wi

[ccp4bb] Structural biology faculty search at UC-Davis

Dear Colleagues, The Molecular Cellular Biology department at the University of California, Davis is searching for two tenure track faculty at the assistant professor level in many areas, including structural biology. The UC-Davis College of Biological Sciences is an excellent environment fo

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

You can take XDS data into Pointless & Aimless (the CCP4 Data Reduction task) either from the unscaled INTEGRATE.HKL or the scaled XDS_ASCII.HKL file (or files). In the case of a single XDS_ASCII.HKL you don't need to rescale it in Aimless, though you can if you want. Aimless uses a similar but

[ccp4bb] CCPBioSim one day training workshop on free energy calculations

Dear all, CCPBioSim are running a free one-day training course on performing free energy calculations in protein systems. The particular focus will be on estimating protein-ligand binding affinities, but the role of solvation in mediating protein-ligand interactions will also be explored. Date

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT s

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan wrote: > Hi, > > I actually choose the option 'constant' further

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'.           Boaz     Boaz Shaanan, Ph.D. Dept. of Life Sciences  Ben-G

[ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Hello all, in a discussion on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specif

Re: [ccp4bb] workstation crystallography

I will comment on specific features you might look for in a crystallographic workstation, rather than brand names. I usually build from parts rather than buy intact machines. CPU: 3+ GHz per compute core is good these days. For a standard single user desktop, 4 CPU cores is fine. More cores wi

Re: [ccp4bb] workstation crystallography

I'm running home-built Ubuntu boxes with old, plain-vanilla CPUs (e.g., Q9300 or core i3/i5/i7) and 6-8Gbyte of RAM, and a cheap Nvidia video card (e.g. GT 9xxx or GT 620).This is more than sufficient to do routine structure solution. Any contemporary desktop or laptop computer should be suffic

Re: [ccp4bb] Amino acid side chains without density

Dear Sasha, you should bear in mind that the major part of users of your deposited structure will not be crystallographers, and they probably don't know what e.g. a B-value is. So also may no use Coot to visualise the structure hence may not be pointed at graphically that occupancies are set to ze

[ccp4bb] workstation crystallography

Dear ccp4 bb members, I need to buy a desktop workstation for the purpose of running crystallography related applications. I have short-listed HP's Z420 and Dell's T7600, I chose this because their configuration description looks impressive (8 cores, 16 threads, 3.6 GHz processor etc.). However, I

Re: [ccp4bb] Amino acid side chains without density

Hi Sasha, this has been discussed on this list in the past, on several occasions. If a consensus has been achieved, I've missed that. For what it's worth, I don't see why you'd remove a side chain or set the occupancy to 0 without experimental evidence for its absence or non-occupancy. I l

Re: [ccp4bb] Amino acid side chains without density

Dear Sasha, There was a survey done by Ed Pozharski back in 2011 The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set

Re: [ccp4bb] Amino acid side chains without density

I think you'll find that this is not a naive question.. I doubt there is a consensus for this. Neither option is ideal, mainly because of possible confusion generated for non-crystallographers. My preference is to include the side chain but set the atoms i do not see to zero occupancy. The P

[ccp4bb] Amino acid side chains without density

Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?

Re: [ccp4bb] Incubator for crystallization

Dear Ulrike, Molecular dimensions incubator model MD5-601 works pretty good in our lab. -Peltier type -low vibration -fully programmable up to 99 days -temperature up to 4C -accommodate low space -with RS232 Check the following links | From archives related to your question posted previously.

[ccp4bb] Incubator for crystallization

Hi everybody, I want to buy a smaller incubator for protein crystallization (30-50 l). Do you have any recommendations ? Do you prefer specialized incubator models with low vibration or are you just using standard incubators ? Best wishes, Ulrike