[ccp4bb] The oldest science

2021-03-31 Thread David Schuller
https://www.haaretz.com/archaeology/.premium-somebody-in-the-kalahari-had-a-crystal-collection-105-000-years-ago-1.9670735 Somebody in the Kalahari Had a Crystal Collection 105,000 Years Ago -- === All Things Serve the Beam

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread David Schuller
demic Paralyzes Human Race, Fuels Contention, Kills Millions, Drives the Rest Mad?" JPK On Wed, Feb 17, 2021 at 12:40 PM David Schuller <mailto:schul...@cornell.edu>> wrote: I read that book. It does not end well. On 2/17/21 12:33 PM, Jacob Keller wrote:

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-17 Thread David Schuller
I read that book. It does not end well. On 2/17/21 12:33 PM, Jacob Keller wrote: It would seem to me that it should be possible to generate versions of the Covid virus that would: A. be extremely contagious and yet B. be clinically benign, and C. confer immunity to the original covid virus.

Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

2020-12-04 Thread David Schuller
We use aquarium gravel for this purpose. It does not have the fine dust-like particles that normal construction gravel might. On 12/4/20 11:42 AM, Nukri Sanishvili wrote: Hi John, I think I know what might have happened: Many of the MX beamlines at the APS use some sort of filler in the

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread David Schuller
There are cases where cell dimensions vary in a very real way. I have a system in which the unit cell volume can differ by more than 10%. When I first explored this system in the long ago times, before cryo-crystallography was a thing, the unit cell dimensions would change during data

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

2020-07-03 Thread David Schuller
We routinely use NoMachine NX or X2Go to share the desktop for remote data collection. And recently I have personally collected data using such while simultaneously running a Zoom window for communication. Internet speed to my home is about 100 Mbps download, 11 Mbps upload. A few notes: If

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

2020-06-30 Thread David Schuller
By all means, if you still have "disks" you should get rid of them, and replace them with some modern storage. On 2020-06-29 21:17, Edward A. Berry wrote: Now can we get rid of all the superfluous disks in our RAID? Or at least not replace them when they fail? On 06/29/2020 06:24 PM,

Re: [ccp4bb] number of frames to get a full dataset?

2020-06-22 Thread David Schuller
The old saying was degrees, not frames. If your frame width is not 1 degree, the result will differ accordingly. One factor is whether the detector is centered or offset, and whether it is large enough to get the entire pattern. If the detector is offset, you are not getting the full

Re: [ccp4bb] disinfecting keyboards

2020-04-29 Thread David Schuller
If you are going that route, it would make sense to locate the UV lamps in the X-ray hutch, since those already have safety interlocks, etc. The X-ray beam itself is too directional to uniformly cover much. On 2020-04-29 15:48, Eduardo Rodríguez-Román wrote: Hi Tim, It may be convenient to

Re: [ccp4bb] CCP4 7.1 released

2020-04-23 Thread David Schuller
Coincidentally, Python 2 had its final release just a few days ago. I trust python components of CCP4 are all now using Python 3. https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/ - === All Things Serve the

Re: [ccp4bb] Methods to improve ligand density of a homodimer?

2020-04-20 Thread David Schuller
It sounds like you are looking for MAPROT. http://www.ccp4.ac.uk/html/maprot.html On 2020-04-20 15:23, Kyle Gregory wrote: Hello all, I have a homodimer structure in P1 21 1 spacegroup, the dimer is likely a crystallographic artefact, where it looks like the monomer is rotated by ~ 180

Re: [ccp4bb] MX data processing with GPUs??

2020-02-19 Thread David Schuller
Thank you for the info. Another of the Threadripper 3xxx series, the 3990X has 64 cores for 128 threads, so perhaps it is time to raise that 99*99 limit in XDS. On 2020-02-19 07:21, Kay Diederichs wrote: Dear Ana, it is easy to ask the question (and I've been asked several times), but

[ccp4bb] Explore your inner lattice

2019-10-08 Thread David Schuller
https://www.cnet.com/news/diamonception-miners-find-diamond-trapped-inside-another-diamond/ Diamonception: Miners find diamond trapped inside another diamond -- === All Things Serve the Beam

Re: [ccp4bb] Shelx and debian 10

2019-10-08 Thread David Schuller
There is now another alternative. There are platforms for packaging software with necessary libraries. PyMOL for example is available using "snap". https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg46623.html On 2019-10-08 06:21, George Sheldrick wrote: As explained in the attached

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

2019-07-22 Thread David Schuller
On 7/22/19 3:40 AM, Bärbel Blaum wrote: "As I said, the lead author may not actually be the crystallographer here" Bärbel No need to wonder, that info should be in the PDB file header. The author of the coordinates is not necessarily the same as the author of the primary reference. --

Re: [ccp4bb] [COOT] guile: error while loading shared libraries: libguile.so.17: cannot open shared object file: No such file or direct

2019-05-23 Thread David Schuller
From a Scientific Linux 7 system: #> yum --enablerepo=epel --enablerepo=elrepo whatprovides "*/libguile.so.17" ... epel/x86_64/filelists_db |  11 MB 00:01 compat-guile18-1.8.8-14.el7.x86_64 : A GNU implementation of Scheme for    : application extensibility

Re: [ccp4bb] crystals mounted in microRT capillaries

2019-05-17 Thread David Schuller
How far are you sending them? If they go by aircraft, they may experience unexpected pressure differentials and temperature extremes. On 5/17/19 2:20 AM, Michael Colaneri wrote: Dear all, how can one mail crystals mounted in loops using the microRT capillaries of Mitegen? Thank you. Mike

Re: [ccp4bb] PyMOL now packaged as a snap on Linux

2019-05-16 Thread David Schuller
It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should also work on RHEL7 and Centos 7) Thank you. On 5/16/19 10:47 AM, Darren Hart wrote: Some more info: https://snapcraft.io/pymol-oss It seems to work exactly as expected. Darren On 16/05/2019 16:05, Folmer

[ccp4bb] 3D

2019-03-11 Thread David Schuller
https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/ NVIDIA will stop supporting 3D glasses in April -- === All Things Serve the Beam ===

Re: [ccp4bb] Clear Linux

2019-02-07 Thread David Schuller
I would be wary of an OS developed and promoted by a hardware manufacturer (Intel). The Phoronix benchmarks you linked were conducted on an Intel Xeon chip. I wonder how Clear OS performs with AMD chips, which are featuring very attractive performance and price recently. On 2/7/19 10:38 AM,

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

2018-12-20 Thread David Schuller
I can see two possible paths here: 1) Make the card work with an emitter or 2) Switch to a monitor with a built-in emitter Datasheet on the graphics card:

Re: [ccp4bb] Fedora 29 breaks CCP4

2018-11-01 Thread David Schuller
Does this depend on which desktop is used? We have been using the MATE desktop rather than the default Gnome. On 10/31/18 10:21 PM, Andrey Lebedev wrote: Dear CCP4 users, The recently released Fedora 29 breaks all the CCP4 graphical components (interfaces and update manager). This is

[ccp4bb] Sulphate or phosphate?

2018-07-31 Thread David Schuller
How can one distinguish between a sulphate or phosphate in an electron density map? Both are present in the mother liquor, and resolution is in the range of 1.75 - 2.25 A -- === All Things Serve the Beam

[ccp4bb] Might be of interest to this group

2018-02-09 Thread David Schuller
http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9 A Novel Form of Stereo Vision in the Praying Mantis Vivek Nityananda,Ghaith Tarawneh, Sid Henriksen,Diana Umeton,Adam Simmons, Jenny C.A. Read DOI:

Re: [ccp4bb] Super protein wire model bender

2018-01-09 Thread David Schuller
I think those used to be sold by the Charles Supper Co. Check out their cat# 7145 http://www.charles-supper.com/en/page/product.cfm?idProduct=33 On 01/09/18 03:34, syed ibrahim wrote: Dear Friends I am looking for the provider details of instrument - Byron Bender (or super protein wire

Re: [ccp4bb] 3D stereo and pymol

2018-01-03 Thread David Schuller
The Mate desktop should also work; it is a continuation of the old Gnome 2 desktop. - dave schuller On 01/03/18 04:42, Wim Burmeister wrote: I answer a bit late, but I repost a message on 3D graphics from Mai 2017 : Hello, we just wanted to share our experience in finding a configuration

Re: [ccp4bb] Radiation damage to the FAD in enzyme structure

2017-11-06 Thread David Schuller
Some alternative interpretations have been suggested, but if you think you are seeing radiation damage, you could try collecting data on several crystals and binning it by dose received. For comparison see: The catalytic pathway of horseradish peroxidase at high resolution. Berglund, et al.

Re: [ccp4bb] Clean Ubuntu system disk

2017-06-13 Thread David Schuller
I like to pipe the `du` output straight into a `sort` command. That way the biggest directories appear at the end. cd / sudo du -sk * |sort -n That is for directories. If you are looking for the largest files, you can try something like this: ls -lR |sort -nk5 On 06/13/17 04:31, Arnaud

Re: [ccp4bb] mystery disappearance of CCP4 website(s)

2017-05-25 Thread David Schuller
I can't reach it. A newspaper site I frequent, www.startribune.com, was down earlier this morning, but is back up already. On 05/25/17 09:12, Andrew Sharff wrote: You are not alone. They are unreachable from here too! Andrew On 25/05/17 14:09, R. Michael Garavito wrote: I have been

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread David Schuller
I wonder if anyone has tried glutamate as a cryprotectant for proteins. If the [] is that high, it may make a stable environment for proteins. I have no idea what effect it might have on ice formation. https://amb-express.springeropen.com/articles/10.1186/2191-0855-3-36 /Bacillus subtilis/

[ccp4bb] Citing the literature

2016-12-23 Thread David Schuller
I looked with distaste at the pile of notes I'd accumulated for my next Revere High Science Club lecture, on crystallography, which had been my specialty in graduate school and for many years after. The Carbon Murder, "A Gloria Lamerino Mystery" by Camille Minichino, 2004, ISBN 0-373-26522-0

Re: [ccp4bb] AW: unusual monoclinic relation?

2016-12-19 Thread David Schuller
On 12/19/16 11:25, herman.schreu...@sanofi.com wrote: Dear Andy, I don’t think you will solve this pre-Xmas ... There is hope of a pre-Christmas solution. Convert to Eastern Orthodox; that will provide an extra two weeks margin, due to the Orthodox use of the Julian calendar. --

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

2016-12-16 Thread David Schuller
"The proteins are stoichiometric" Huh? What is the stoichiometry? I'm expecting a ratio here, like 1:1 or some such. I see two possibilities: 1) The two proteins are completely interchangeable in the structure. 2) The two proteins are not interchangeable, but are being

Re: [ccp4bb] Unfilled electron density for structure with tNCS

2016-11-30 Thread David Schuller
There are reasons why MR might fail to find additional copies; perhaps a surface loop in the search model interferes with packing. You should probably take a look at solvent content. On 11/30/2016 12:20 PM, Matthew Bratkowski wrote: Hello all, I am working on a structure in space group P4

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

2016-10-28 Thread David Schuller
The last I heard (which was a while ago), Windows could run the stereo emitter over USB with a Geforce card, but Linux still needed a Quadro card with the 3 pin mini-DIN connector. I hope this is no longer true, but I have not heard clear information to the contrary. Note that the text you

[ccp4bb] Dials

2015-07-08 Thread David Schuller
Does this look like a suitable solution for those who like dials while model building? http://petapixel.com/2015/07/07/review-palettes-modular-photo-editing-controls-are-pricey-but-powerful/

Re: [ccp4bb] Point group

2015-05-21 Thread David Schuller
On 05/21/15 11:56, Mohamed Noor wrote: Dear all I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. MR searches and refinement in

Re: [ccp4bb] CYS mod

2015-05-12 Thread David Schuller
So far almost everyone is suggesting BME. I didn't do the purification crystallization myself, but I am told: Buffer was HEPES cryo was ethylene glycol, glycerol and DMSO. Some MgSO4 and KPO4 No BME, but maybe some DTT. Purified from a proteobacterium. On 05/12/15 15:20, Dyda wrote: What

Re: [ccp4bb] No MR solution

2015-04-01 Thread David Schuller
On 04/01/15 11:23, Roger Rowlett wrote: There are 8 possible space groups in the P422 family. Did you search in all of these? What he said. The answer should be YES. Phaser is set up to do this easily. How many search models are likely to fit in the unit cell based on Matthews analysis?

Re: [ccp4bb] nVidia quadro

2015-03-25 Thread David Schuller
You could check the nVidia page of officially supported displays. It includes a search tab so you can check for Built-in Emitter. http://www.nvidia.com/object/3d-vision-displays.html Performing that search brings up 5 contenders. Good luck finding any of these products still for sale. On

Re: [ccp4bb] chloride or water

2015-01-21 Thread David Schuller
On 01/21/15 15:04, Pavel Afonine wrote: (And why not make every water into UNX for good measure as well?) Why not indeed, except that I would not call it water but Dummy Atom with an element type of your choice. there was a time long ago when budding crystallographers were taught to

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

2015-01-09 Thread David Schuller
On 01/09/2015 12:11 AM, Jens Kaiser wrote: In addition to what others have -- correctly -- stated I want to add one more thing: Yes, you are right, if you do not get your hands on a monitor with built-in emitter, you'll need ad least a K4000 and in many cases the VESA din bracket (~$50). You do

Re: [ccp4bb] Demonstration for 2nd graders?

2015-01-08 Thread David Schuller
This one is probably above second grade, but the equipment setup is pretty easy http://ipl.physics.harvard.edu/wp-uploads/2013/03/15c_s07_5.pdf Measuring the wavelength of light with a ruler On 01/08/15 13:35, John Lee wrote: Hi everyone, Slightly off topic here but I got myself

Re: [ccp4bb] HKL2000 Display

2014-12-03 Thread David Schuller
Yes, it is probably the wrong detector type, or the wrong parameters, perhaps binned vs. unbinned. On 12/03/14 07:25, David Waterman wrote: Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I

Re: [ccp4bb] are mathematician scientists ?! (previously Free Reflections as Percent and not a Number)

2014-11-29 Thread David Schuller
On 11/29/14 07:47, Alexandre OURJOUMTSEV wrote: Dear Tim, as you know I avoid making public comments and prefer enjoying the comments done by others, however this time is hard to resist :-) I was surprised by your mail : do you mean that mathematicians are NOT SCIENTISTS ?! Do you mean that

Re: [ccp4bb] Formulation of my own mother liquor

2014-11-21 Thread David Schuller
The most important thing is that you do it the same way every time. But you might also put some thought into flexibility, in case you need to explore cryoprotectants, etc. On 11/21/14 11:48, amro selem wrote: Dear All, first i wish you nice weekend, then i wanna ask about formulation of my

Re: [ccp4bb] how to combine two derivative datasets that are not isomorphous?

2014-11-18 Thread David Schuller
You don't mention any quality indicators on your derivatives, nor resolution. Presuming they actually have some decent phasing power, you may be able to generate phases maps using SIR phasing + solvent flattening. If you can do that for each isomorphous set, then you could combine them using

Re: [ccp4bb] workstation crystallography

2014-11-11 Thread David Schuller
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

Re: [ccp4bb] Molecular Replacement model preparation

2014-10-05 Thread David Schuller
Since there is a hinge, you could try searching with the two domains separately. On 10/05/14 03:34, Luzuokun wrote: Dear all, I’m doing molecular replacement using Phaser. My protein is predicted to have two domain with a “hinge” linking them. The model sequence identity is 0.27. But the MR

Re: [ccp4bb] Space group numbers

2014-10-02 Thread David Schuller
With the successful introduction of racemic crystallization to macromolecular, a large number of possible space groups have been opened up to this audience. You can find examples in the PDB of space groups P -1 (i.e. P 1-bar), I -4 2 d, etc. On 10/02/14 06:51, George Sheldrick wrote: The

Re: [ccp4bb] L-Dopa Stabilization?

2014-07-03 Thread David Schuller
On 07/03/14 17:05, Edward A. Berry wrote: I see, L-dopa is a phenolic (o-quinolic actually) compound, same as what gets oxidized in sliced apples to turn them brown. At least, that's the way it used to be. http://www.okspecialtyfruits.com/arctic-apples/about-our-nonbrowning-apples Truly

[ccp4bb] FORTRAN still rules?

2014-05-08 Thread David Schuller
http://arstechnica.com/science/2014/05/scientific-computings-future-can-any-coding-language-top-a-1950s-behemoth/ Scientific computing's future: Can any coding language top a 1950s behemoth? Cutting-edge research still universally involves Fortran; a trio of challengers wants in. ---

Re: [ccp4bb] small molecule crystallography

2014-03-24 Thread David Schuller
Coincidentally, I just spent my day trying to index a lattice of ~ 10 x 10 x 11 A. Mounting samples: if the compound is stable, just glue it to the end of a steel pin. No muss, no fuss. We had to attenuate our synchrotron beam heavily to make it work; motors can only turn so fast. We did

Re: [ccp4bb] account creation for CCP4wiki (and XDSwiki)

2014-03-12 Thread David Schuller
On 03/12/14 11:52, Kay Diederichs wrote: ... Account creation now uses a Captcha which is not of the boring type, but rather challenges your expertise in telling cats from dogs. I have heard that this algorithm can be fooled by cosmetic surgery.

Re: [ccp4bb] preparation of citrate buffer pH3-6.5

2014-01-30 Thread David Schuller
RE citrate buffer preparation The Calbiochem buffers has some generally useful information about buffers; pKa and such. http://www.antibodybeyond.com/books/Calbiochem_Buffers_Booklet_CB0052_E.pdf http://wolfson.huji.ac.il/purification/PDF/Buffers/Calbiochem_Buffers_Booklet.pdf --

Re: [ccp4bb] Phasing with Many Monomers/AU

2014-01-20 Thread David Schuller
Is the monomer the biggest unit you have to search with? If there is a dimer, tetramer, etc. that is conserved, you could try searching with that. On 01/19/14 14:30, Chris Fage wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my

Re: [ccp4bb] A question on crystal optimization

2013-12-25 Thread David Schuller
I don't know why you would concern yourself with the outward morphology of the crystal, rather than its diffraction quality. I have grown some gorgeous little gems which did not diffract well. On 12/24/13 23:49, Acoot Brett wrote: Dear All, I am optimizing a crystal. In one of the

[ccp4bb] Heavy atom sites

2013-12-15 Thread David Schuller
I have some SIRAS data of a known structure. I want to get the isomorphous and anomalous occupancy and phasing power from my data. What's the best software to do this? -- === All Things Serve the Beam

Re: [ccp4bb] Stereo monitor

2013-11-21 Thread David Schuller
On 11/21/13 07:50, mesters wrote: ...(both handle the dual link DVI-D standard)... Are there any monitors on the market yet which can produce stereo 3D from a Displayport 1.2 input? With or without a built-in emitter. --

[ccp4bb] Fred Sanger obit

2013-11-20 Thread David Schuller
http://www.bbc.co.uk/news/science-environment-25020112 Frederick Sanger: Double Nobel Prize winner dies at 95 -- === All Things Serve the Beam ===

[ccp4bb] Fourier transforms

2013-11-18 Thread David Schuller
http://nautil.us/blog/the-math-trick-behind-mp3s-jpegs-and-homer-simpsons-face The Math Trick Behind MP3s, JPEGs, and Homer Simpson's Face Posted By Aatish Bhatia on Nov 06, 2013 -- === All Things Serve the Beam

Re: [ccp4bb] bluetooth monitor

2013-10-29 Thread David Schuller
IMHO Bluetooth is way too slow for a monitor connection. On 10/29/2013 01:05 PM, Brett, Thomas wrote: Hi all: I was wondering if anyone had economical suggestions on a bluetooth LED or LCD monitor. I would like to have a wall mounted monitor that one could easily connect laptops and imacs to

Re: [ccp4bb] bluetooth monitor

2013-10-29 Thread David Schuller
The best technology would be Wigig, but I don't think it's on the market yet. Some wireless monitor connection solutions appear to be available using Intel WiDi and Miracast. Check your favourite vendor for availability and requirements. On 10/29/2013 01:05 PM, Brett, Thomas wrote: Hi

Re: [ccp4bb] About molecular replacement

2013-09-12 Thread David Schuller
Perhaps some correct solutions were thrown out due to packing considerations. There are a few methods to address that possibility. You could use a search model with large loops trimmed, especially is a sequence comparison shows they are probably not conserved. Or you could search with a

Re: [ccp4bb] non-diffracting xtals

2013-08-19 Thread David Schuller
On 08/19/13 16:49, Mahesh Lingaraju wrote: Hello people I recently obtained hexagonal rod like crystals (150x50x20 um) which turned out to be non diffracting. What is the usual convention for cases like this ? do people usually give up on the condition or still try to optimize it ? It

Re: [ccp4bb] 5D data storage

2013-07-12 Thread David Schuller
It seems like every couple of years I see an article about a new high density optical format. Then they don't make it to the marketplace. I think it has something to do with resistance from the music movie business over piracy concerns. But anyway, I have learned not to get too excited until

[ccp4bb] Stereo images

2013-07-04 Thread David Schuller
http://io9.com/rare-3d-camera-found-containing-photos-from-wwi-669397198 Rare 3D Camera Found Containing Photos from WWI http://io9.com/rare-3d-camera-found-containing-photos-from-wwi-669397198 -- === All Things Serve the

Re: [ccp4bb] Extracting .pdb info with python

2013-06-06 Thread David Schuller
You could use FORTRAN. It's good at formatted I/O. On 06/06/13 00:37, GRANT MILLS wrote: Dear CCP4BB, I'm trying to write a simple python script to retrieve and manipulate PDB data using the following code: #for line in open(PDBfile.pdb): #if ATOM in line: #column=line.split() #

Re: [ccp4bb] atomic coloring for the color blind

2013-06-01 Thread David Schuller
How about Braille for those who are blind to all colours? -- === All Things Serve the Beam === David J. Schuller

Re: [ccp4bb] Diffraction image viewer with display of resolution circles

2013-05-23 Thread David Schuller
The version of ADXV we have has some nice resolution ring features. There is a mode with the typical 5 rings of evenly spaced resolution. There is Anchor1 which draws a circle about the beam centre and through a selected point. There is Pick3 which constructs a circle from 3 selected points.

Re: [ccp4bb] Cauliflower looking crystals

2013-05-06 Thread David Schuller
I haven't seen cauliflower but I have seen brussel sprouts. Condtions (esp. pH) were changing over the course of crystallization, and the stalks and sprouts were different crystal forms. On 05/06/13 06:17, Browning Christopher wrote: Hi Everybody, I was wondering if anybody had a similar

Re: [ccp4bb] detectors on home sources

2013-04-30 Thread David Schuller
The Excillum MetalJet (TM) source is technically very interesting, with its liquid metal jet anode, but I have no idea how well it works for typical in-house crystallography use. On 04/30/13 15:00, Fareed Aboul-Ela wrote: I'm involved in advising my institute on an X-ray home source for a

Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit

2013-04-29 Thread David Schuller
On 04/29/13 12:26, Roger Rowlett wrote: FYI, I do know of one example of a solved structure where some of the molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules in the ASU have low B-factors (mid 30s) and 4 have high B-factors (50s-60s). In the unit cell these layers

[ccp4bb] Crystals in the news

2013-04-29 Thread David Schuller
http://news.discovery.com/earth/rocks-fossils/sea-squirt-crystal-solved-130429.htm Crystal Puzzle Solved with Sea Squirt RE vaterite Science 26 April 2013: 454-457.[DOI:10.1126/science.1232139]

Re: [ccp4bb] CCP4 Update victim of own success

2013-04-11 Thread David Schuller
On 04/11/13 13:36, Ethan Merritt wrote: On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote: Eugene - that's great. I too run a small suite of Macs (12) and was trying to find a practical way of updating all those machines remotely. The command line version of CCP4um will be very

Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

2013-03-20 Thread David Schuller
On 03/20/13 13:25, Kyriacos Petratos wrote: Dear All, we have two data sets at about 0.9 and 1.9 Ang. resolution collected from a single crystal. Integration with iMosflm seems to be fine like the scaling within each of the data sets. When we try to merge and scale both of them with 'Scala'

Re: [ccp4bb] Philosophical question

2013-03-19 Thread David Schuller
On 03/19/13 10:34, Jacob Keller wrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident- QWERTY didn't just happen. It was designed. Don't kids today know how to use

Re: [ccp4bb] Philosophical question

2013-03-19 Thread David Schuller
On 03/19/13 14:41, Jacob Keller wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA (protein and DNA sequences, etc). To make it logically sound, I think you have either to include some kind of super-high boundary to getting to other

Re: [ccp4bb] stereo monitor for DELL T7600

2013-03-01 Thread David Schuller
On 03/01/2013 06:52 AM, mesters wrote: Just make sure the graphics card has not only miniDisplay connectors... The 3D monitors mostly have HDMI and DVI-D. Do not confuse the DVI-D with single/simple DVI as the bandwidth will be too low for stereo. 1) Monitors with 120 Hz stereo support

Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!

2013-02-17 Thread David Schuller
On 02/16/13 00:46, Zhijie Li wrote: Hi Jacob, Interesting topic. This reminds me the posters I saw on ACA 2010, on the femto-second infrared laser based instrument . That instrument utilizes the nonlinear optical properties of crystals of chiral molecules to detect very small crystalline

Re: [ccp4bb] electron density assignment

2013-02-04 Thread David Schuller
Generate an anomalous map and look for peaks. Many metals would generate anomalous. On 02/04/13 07:39, Gang Dong wrote: Dear all, Here are some hexmeric densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in

Re: [ccp4bb] off topic - legacy hardware help needed

2013-01-24 Thread David Schuller
On 01/24/2013 03:19 AM, James Stroud wrote: It seems like the problem is that the Indigo has an IP address that is not part of the subnet that it is on, so this makes network access impossible. Is this correct? If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on a

Re: [ccp4bb] Crystallography Near Absolute Zero?

2013-01-23 Thread David Schuller
On 01/23/13 10:11, Jacob Keller wrote: Is anyone aware of any datasets taken at near absolute zero? I was wondering what would happen... http://www.ncbi.nlm.nih.gov/pubmed/12718921 New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium.

[ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-18 Thread David Schuller
http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Golden Jubilee of Ramachandran Plot http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Exactly fifty years from now i.e. in the year 1963, G. N. Ramachandran et. al published

Re: [ccp4bb] Crystallization buffer pH optimization

2013-01-17 Thread David Schuller
That may be the CALBIOCHEM Buffers Booklet, which is free online as a PDF. On 01/17/2013 12:38 AM, Mike John wrote: Hello, Shameful and sorry for asking this simple question, it looks like this when first starting a new setup in so-called structural biology. I remmeber a book of, probably,

Re: [ccp4bb] [COOT] favorite linux flavor, or as most of you would say, flavour ;)

2013-01-17 Thread David Schuller
A year or two ago we switched from Fedora to Scientific Linux 6. It is a free repackaging of Red Hat Enterprise, so it should be a straightforward shift from Fedora. It is supported long term, and has backing from several large labs (fermilab, CERN, etc) CCP4, Coot, etc. seem to be

Re: [ccp4bb] protein degradation in crystal

2013-01-16 Thread David Schuller
Were the crystals which run different on gels from the same drop, or separate drops? Yes, it is possible that the protein is being cleaved in the crystal (self-cleavage?); but it may also be that it is being cleaved in the mother liquor, and that crystallization is enriching one form or

Re: [ccp4bb] protein degradation in crystal

2013-01-16 Thread David Schuller
Were the crystals which run different on gels from the same drop, or separate drops? Yes, it is possible that the protein is being cleaved in the crystal (self-cleavage?); but it may also be that it is being cleaved in the mother liquor, and that crystallization is enriching one form or

Re: [ccp4bb] Today ...

2012-12-21 Thread David Schuller
On neither case does an alphanumeric sort coincide with a chronological sort. The obvious solution is to petition to have the months renamed alphabetically. On 12/21/12 03:23, Tom Murray-Rust wrote: Hi Juergen, Your scheme as printed has two J's - so January and July are indistinguishable!

Re: [ccp4bb] Today ...

2012-12-20 Thread David Schuller
On 12/20/12 11:23, Edward A. Berry wrote: No, No- in scientific circles we go from MSB on the left to LSB on the right: 2012 12 20 (still a sort of palindrome). This is the best method if you are going to incorporate the date into a file name. That way alphanumeric and chronological

Re: [ccp4bb] hkl2000 install

2012-11-19 Thread David Schuller
On 11/18/12 20:48, 王瑞 wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ?

Re: [ccp4bb] vitrification vs freezing

2012-11-16 Thread David Schuller
On 11/16/12 17:33, Adrian Goldman wrote: Bernard Dixon is merely copying the great essay by George Orwell 'politics and the english language'. Its well worth a read. In it, Orwell lays out about six simple rules for writing good english prose. Three of them are: never use the passive voice.

[ccp4bb] Sutherland wind Kyoto pPrize

2012-11-11 Thread David Schuller
http://www.i-programmer.info/news/82-heritage/5061-ivan-sutherland-presented-with-kyoto-prize.html Dr Ivan Sutherland, often dubbed Father of Computer Graphics was one of three laureates honored at the 28th Annual Kyoto Prize Ceremony held today in Japan, The Kyoto Prize

Re: [ccp4bb] Assemble Protein-DNA complex

2012-11-09 Thread David Schuller
On 11/09/12 15:43, Tommi Kajander wrote: It is not very surprising that the affinity gets higher with lower salt, right? Not at all. I wanted to ask if their assay could distinguish between specific binding and nonspecific binding, but I decided not to sidetrack the discussion. --

Re: [ccp4bb] Ca or Zn

2012-10-30 Thread David Schuller
On 10/30/12 15:02, Bosch, Juergen wrote: calculate an anomalous map, you should see the Zn signal even if you collected at the SeMet peak. Jürgen .. Ca can have a noticeable anomalous signal of its own, if your data are good. If the possibility to collect new data exists,

Re: [ccp4bb] Stout and Jensen

2012-10-22 Thread David Schuller
I note that it is on sale at Amazon.com for only $177.07 right now. On 10/22/12 14:36, Jayashankar wrote: Dear All, I would like to buy the book '' X-ray structure determination'' by George.H.Stout and Lyle.H.Jensen. If in any case , somebody has shelved it and want to give away for

Re: [ccp4bb] Help Please!

2012-09-18 Thread David Schuller
Those commands which do not work apparently require the version of libc that you replaced. If your description is accurate, you did not actually delete the file, but merely renamed it. You can boot up from your Linux (this is Linux, right?) installation disk in RESCUE mode and put the file

Re: [ccp4bb] CCP4-6.3.0 installation

2012-08-04 Thread David Schuller
On 08/04/2012 04:38 PM, james09 pruza wrote: Dear CCP4bbers, I am facing CCP4-6.3.0 installation problem. Unable to run make. Configuration is done. Getting error while running make (command not found). Please help. Thanks in advance, James Which operating system are you using? On

Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure

2012-08-02 Thread David Schuller
I do not have the reference you are seeking, but I have seen cacodylate-containing xtals diffract to better than 1.2 and hold up very well. Also, arsenic has an anomalous signal which may be exploited for phasing, peak ~ 1.04 A. On 07/29/12 18:53, Tatyana Sysoeva wrote: Hi! I heard a

Re: [ccp4bb] harvesting in cold room

2012-07-13 Thread David Schuller
On 07/13/12 17:29, Jacob Keller wrote: You probably already know this, but nitrogen is not at all poisonous--about 78% of the air is nitrogen. I guess you were probably worried about asphyxiation? We have oxygen sensors in our X-ray hutches for precisely that reason. --

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