Re: [ccp4bb] A crystallographer on Mars

2013-05-07 Thread Jim Pflugrath
Most participants in the CSHL X-rays Methods in Structural Biology course have seen the powerpoint presentation of Alex McPherson's trip to Mars in 2001. Here are a couple of slides from the presentation: (Trehalose was

Re: [ccp4bb] reference for true multiplicity?

2013-05-14 Thread Jim Pflugrath
Precision does not trump accuracy is something Michael Blum told me. Also Charles Wheelan wrote in his recently published Naked Statistics: “But no amount of precision can make up for inaccuracy.” I myself have been pleasantly surprised at how low multiplicity can be nowadays and still do

[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 14-29, 2013: Application deadline June 15th

2013-05-29 Thread Jim Pflugrath
Hey Everybody, I wanted to draw your attention again to the upcoming application deadline on June 15, 2013 for the CSHL X-ray Methods in Structural Biology Course to be held October 14-29, 2013. Also please also pass this on to any colleagues, friends, professors, research associates, grad

Re: [ccp4bb] Crystallisation below 0°C

2013-05-30 Thread Jim Pflugrath
If one has cryoprotectant in their conditions, one may be surprised that crystals can grow at -20 deg C and probably lower. Practice with lysosyme. :) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Glenn Masson [] Sent:

Re: [ccp4bb] anomalous scattering server down?

2013-06-01 Thread Jim Pflugrath
How does that compare to something that readily works with Fe, such as horse hemoglobin on a home lab copper X-ray system with 2 Fe in 291 residues in the asymmetric unit? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry

Re: [ccp4bb] HKL2000 sigma cutoff

2013-07-07 Thread Jim Pflugrath
I wonder if the rejects file had a large number of reflections in it in one case, but not in the other case. One can be playing with various options and create or add to such a large list. That's why there is the Delete Reject file option. Jim From:

Re: [ccp4bb] Resolution, R factors and data quality

2013-08-27 Thread Jim Pflugrath
I have to ask flamingly: So what about CC1/2 and CC*? Did we not replace an arbitrary resolution cut-off based on a value of Rmerge with an arbitrary resolution cut-off based on a value of Rmeas already? And now we are going to replace that with an arbitrary resolution cut-off based on a

Re: [ccp4bb] from sca to CC1/2

2013-09-18 Thread Jim Pflugrath
The current version of scalepack already calculates CC1/2 and reports it in the log file. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Francesco Angelucci [] Sent: Wednesday, September 18, 2013 5:21 AM To:

Re: [ccp4bb] how to cut back resolution of a well-refined model

2013-10-10 Thread Jim Pflugrath
Please tell me why Rpim should be looked at. Cannot one have meaningless data and have lots of multiplicity to drive Rpim lower without any real benefit? Under what conditions is Rpim useful? And suppose one looks at I/sigI (and not I/sigI) and CC1/2. What of it? And let me write what Phil

Re: [ccp4bb] 100% Rmerge in high resolution shell

2013-11-19 Thread Jim Pflugrath
Graeme wrote: ... Rpim is much more instructive. ... as each of these tells something different. I have to ask: Why is Rpim much more instructive? I'm trying to figure this out still. Can one please summarize what are best practices with all these numbers and how each of these tells

Re: [ccp4bb] ACA 2014 meeting--Session on engaging students in protein crystallography

2014-01-14 Thread Jim Pflugrath
Hi Roger, We have a simple lysozyme project where we collect diffraction images in less than 30 seconds total exposure time and solve the structure by SAD phasing. I've thought that this might make an ideal lab practical: grow crystals one week, everyone collects the data on their own crystal

Re: [ccp4bb] Best compounds for heavy atom soaks

2014-01-15 Thread Jim Pflugrath
And quick iodide soaks may be useful in the 200 mM range. See the sped-up video: Quiz time: What wavelength would give iodide a similar signal to that of selenium? Can one get a better signal than selenium by choosing a different wavelength for

Re: [ccp4bb] Room temperature data collection

2014-02-06 Thread Jim Pflugrath
Clearly, it is always possible to do non-cryogenic data collection simply by not using a cryogenic cooling device and mounting crystals so that they do not dehydrate or dry out. I've been doing quite a lot of room temperature data collection lately because in the home lab we can SAD-phase

Re: [ccp4bb] Room temperature data collection

2014-02-06 Thread Jim Pflugrath
If one is mounting in glass capillaries, we used to put them in a box of blue tips (1000 ul pipetteman tips). Just put a small rolled up wad of kimwipe down in the bottom, so that the capillary does not jam itself down in the narrowing of the tip point. Every capillary gets its own tip and

Re: [ccp4bb] Rmerge of Images

2014-02-13 Thread Jim Pflugrath
I think you are talking about the R of the reflections in an image to the set of unique reflections resulting from scaling. Here is a definition of Rmerge from a dtscaleaverage log file: In the tables below Rmerge is defined as: Rmerge = Sum Sum |Ihi - Ih| / Sum Sum Ih h i

Re: [ccp4bb] Tenure track junior Group Leader Positions in Milan, Italy

2014-04-04 Thread Jim Pflugrath
Thanks for the clarification. I thought at first this position might be related to Dance Your PhD.… Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of

Re: [ccp4bb] AW: [ccp4bb] relation between redundancy and total reflection

2014-04-17 Thread Jim Pflugrath
If one is using the HKL GUI, then click on the menu bar button Report and read the report that is generated. One caveat is that HKL will count any systematically absent reflections in the input files as part of the total number of observations. I forget if scalepack counts the systematically

Re: [ccp4bb] metal ion coordination

2014-04-17 Thread Jim Pflugrath
And what if the site(s) is(are) a mixture of bound metal ions? What if Mg++, Ca++, Na+, Mn++, et al. are bound at the same site(s)? Can the diffraction data rule that out? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique

Re: [ccp4bb] anomalous signal for Mg and Calcium

2014-04-21 Thread Jim Pflugrath
Further to what Nat wrote which I completely agree with, you should tell us the following: 1. Expecting signal of a Calcium atom and expected signal of a Magnesium atom. 2. Are there any intrinsic anomalous scatterers in the structure that you trust such as sulfurs from methionines and

Re: [ccp4bb] shelxd

2014-04-22 Thread Jim Pflugrath
I think what one uses will depend on what one expects to be in the structure and the resolution and the quality of their diffraction data. I usually start with 1.8 Å resolution data in case there is chance of having disulfides. Then 1.9, then 2.4, then 2.0, then 2.6, then 2.2, then 1.85, then

Re: [ccp4bb] anomalous signal

2014-04-25 Thread Jim Pflugrath
d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have solved structures with less multiplicity and lower d/sig. There is a different criteria of signal for when you know the positions of the anomalous substructure atoms and when you need to

Re: [ccp4bb] Confusion about space group nomenclature

2014-05-02 Thread Jim Pflugrath
After all this discussion, I think that Bernhard can now lay the claim that these 65 space groups should really just be labelled the Rupp space groups. At least it is one word. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp

Re: [ccp4bb] report mosaicity

2014-05-16 Thread Jim Pflugrath
HKL-2000 has a menu button at the top Report. If you click on that a report is generated with mosaicity range explicitly listed. It is probably not suitable to describe a crystal as having a single mosaicity value because mosaicity may be anisotropic. It should be obvious that a unit cell

[ccp4bb] New app deadline for CSHL X-ray Methods workshop: July 15, 2014

2014-07-07 Thread Jim Pflugrath
We have extended the application deadline for the CSHL X-ray Methods in Structural Biology Course to be held October 13-28,2014. Our earlier deadline was based on getting all the paperwork completed in time for using NSLS, but since NSLS will not be available*, we can extend the deadline to July

Re: [ccp4bb] Rigaku R-axis IIC X-ray diffraction system

2012-04-14 Thread Jim Pflugrath
The first Rigaku R-AXIS IIC in North America were installed in late 1990 at Yale University and McMaster University. That's the same year the Hubble Telescope went into space and the first search engine Archie was released. The last R-AXIS IIC shipped in 1994. So these are really vintage

Re: [ccp4bb] unique reflections vs unique observations

2012-04-15 Thread Jim Pflugrath
I am aware that some programs report interesting numbers. In addition to what Andrew wrote about resolution cutoffs and truncated reflections, I'd like to mention another issue with systematically absent reflections. The number of observations or reflections that come from an integration

Re: [ccp4bb] Off-pick: suggesiton of puck

2012-04-16 Thread Jim Pflugrath
Rigaku ACTOR robots can accept many different styles of pucks depending on the LN2 dewar baseplate that the particular ACTOR is equipped with. Rigaku in China will sell ACTOR pucks, but if you are looking for ALS-style pucks or ESRF-style pucks or Unipucks or ???, then I am not sure where to

Re: [ccp4bb] effective iodide conc. for SAD data

2012-05-03 Thread Jim Pflugrath
Iodide is a fantastic derivative. One does not need a lot with modern X-ray equipment, careful data collection, and great software. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh Kumar [] Sent: Thursday, May 03, 2012

Re: [ccp4bb] effective iodide conc. for SAD data

2012-05-03 Thread Jim Pflugrath
Please see my poster at the ACA 2012 meeting. See also: (1) Dauter, Z., Dauter, M. Rajashankar, K.R. (2000) Acta Cryst. D56, 232-237. (2) Nagem, R.A.P, Dauter, Z. Polikarpov, I. (2001) Acta Cryst. D57, 996-1002. :) From: CCP4 bulletin board

Re: [ccp4bb] Propane still?

2012-05-21 Thread Jim Pflugrath
Here is a trick which I will attribute to Cambridge: Fill balloon with gas. Put end of balloon over 15 ml Falcon tube. Put Falcon tube in LN2. No wasted gas. I would recommend CF4 or carbon tetrafluoride instead of propane though. CF4 is cheap and non-dangerous. Jim

Re: [ccp4bb] Propane still?

2012-05-21 Thread Jim Pflugrath
As with all reagents used in the lab it is best to understand the health hazards. Thanks for note. Jim From: Jacob Keller [] Sent: Monday, May 21, 2012 5:22 PM To: Jim Pflugrath Cc: Subject: Re: [ccp4bb

[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 15-30, 2012: Application deadline June 15th

2012-06-06 Thread Jim Pflugrath
Once again I wanted to draw everyone's attention to the Cold Spring Harbor Laboratory 2012 X-ray Methods in Structural Biology course which will take place October 15 through October 30, 2012. The official course announcement is here: I think

Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

2012-06-06 Thread Jim Pflugrath
And for more Personal Reflections, one may wish to take a gander at the Rigaku Webinar series with presentations by Brian Matthews and Michael G. Rossmann. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carter, Charlie []

Re: [ccp4bb] cryo for high salt crystal

2012-07-10 Thread Jim Pflugrath
Sucrose, sorbitol, Splenda, trehalose, etc, but instead of 25% (is that w/v or v/w?), try using 100% saturated in reservoir, 75% saturated in reservoir, or 50% saturated in reservoir. You will have to TEST these. See also this webinar on cryocrystallography which shows how to make these

Re: [ccp4bb] Large unit cell, overlaps

2012-07-17 Thread Jim Pflugrath
For large unit cells, one must take particular care with the X-ray beam and the orientation of the crystal. The latter has already been mentioned in previous response. For the beam, some things to do are: 1. Make crystal smaller. 2. Make beam smaller (use a smaller collimator size). 3. Reduce

Re: [ccp4bb] d*trek

2012-08-24 Thread Jim Pflugrath
d*TREK can process single crystal diffraction images from all the common detectors including not only Rigaku detectors, but many different detectors found at synchrotron beamlines around the world such as the APS, ALS, NSLS, CHESS, SLS, ESRF, Diamond, Soleil, PhotonFactory, SPring8, CAMD,

Re: [ccp4bb] Ca or Zn

2012-10-30 Thread Jim Pflugrath
How would you distinguish between a mixture of Ca and Zn in the same locations? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kumar, Veerendra [] Sent: Tuesday, October 30, 2012 1:55 PM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Rpim and how its related to anomalous signal

2012-11-02 Thread Jim Pflugrath
In my opinion Rpim is not related directly to anomalous signal, so perhaps that is why there is some confusion. Also I think some folks confused Rpim with Rrim. The latter is also called Rmeas. But once again, these are not related directly to anomalous signal. I do not find Rpim very

Re: [ccp4bb] low-resolution data and SG

2012-11-04 Thread Jim Pflugrath
This looks like an output from SCALEPACK. Unfortunately, one has no way to know from the output if 21 and 90 are strong intensities or not. One cannot go by the I/sigmaI alone. For example, suppose there is thermal diffuse scatter at these positions or perhaps there is a cosmic ray or

[ccp4bb] What to put on Custom Declaration for shipped samples?

2012-11-06 Thread Jim Pflugrath
I was asked by our shipping folks what we should put on the Customs Declaration so that samples that we ship or that are shipped to us (in dewars, styrofoam boxes, and/or padded envelopes) would not be held up in Customs. I had them put: Scientific samples of less than 1 mg of

Re: [ccp4bb] model protein for ligand soaking

2012-11-10 Thread Jim Pflugrath
Sucrose co-crystallized in lysozyme is wonderful. I think a soak will crack the crystals, but sometimes not. Here's a pic of electron density from an orthorhombic crystal of lysozyme solved in the recent 2012 CSHL X-ray Methods in Structural Biology course:

Re: [ccp4bb] To cryo or not to cryo...

2012-11-30 Thread Jim Pflugrath
Suggestion: What does your plunge of a loopful of the buffer (no crystal) into liquid nitrogen tell you? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu [] Sent: Friday, November 30, 2012 7:22 PM To:

Re: [ccp4bb] protein crystals or salt crystals

2013-02-11 Thread Jim Pflugrath
If one tries to use a dye to determine if crystals are protein or salt, then I recommend that they use both a positive and a negative control. So have some handy salt or sugar crystals ready along with some known protein crystals to use as controls. Jim

Re: [ccp4bb] Diffraction data with big rotation angle

2013-03-14 Thread Jim Pflugrath
5 degrees per image may be problematic for some algorithms since the diffraction spots have uncertain positions in three dimensions. Two dimensions will come from the position of the spot on the detector and the position of the detector. The third dimension will come from the rotation angle

Re: [ccp4bb] High Rmerge and I/sigma values....?

2013-03-29 Thread Jim Pflugrath
As mentioned lots of reasons for this. a. Poor crystal b. Poor mount of the crystal c. Poor equipment or non-working equipment d. Poor maintenance of good equipment e. Improper cryoprotection f. Vibration or movement of goniometer, goniometer head, mounting pin, mounting loop, magnet, etc g.

Re: [ccp4bb] CCP4 Update victim of own success

2013-04-11 Thread Jim Pflugrath
I think James gets to 'fight' like in the old game of rogue by pressing the h, j, k, l keys on his keyboard (not a detachable one either). While Eugene gets to use a modern game controller or a Wii. Ooops, game is already over and James has lost. Jim From:

Re: [ccp4bb] Difficult data

2013-04-16 Thread Jim Pflugrath
Maybe you crystallized something else? Did you look up that unit cell in the PDB? I am having a few issues with a data set I have been working on recently, and was hoping to get some ideas on how to deal with it, if anyone is in the mood. .

Re: [ccp4bb] Differentiating bound Mn Ca.

2007-04-16 Thread Jim Pflugrath
Although the peak height of S atoms can be used as an internal yardstick, one has to worry about differences in occupancy and possibly hetergeneous sites (i.e. Ca, Mn and Mg) which can confuse the interpretation of the results. On Mon, 16 Apr 2007, Eleanor Dodson wrote: In cases like this I

Re: [ccp4bb] .sfrm image files

2007-05-16 Thread Jim Pflugrath
d*TREK from Rigaku can process these images. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yanming Zhang Sent: Wednesday, May 16, 2007 2:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] .sfrm image files Hi, All, I have image files with the format

[ccp4bb] Course: CSHL 2007 X-ray Methods in Structural Biology

2007-06-07 Thread Jim Pflugrath
X-ray Methods in Structural Biology Cold Spring Harbor Laboratory October 15th-30th, 2007 Deadline for applications: June 15th This year marks the 20th time this course has been taught at Cold Spring Harbor Laboratory. It is supported with funds

Re: [ccp4bb] Free travel money: Rigaku announces post-doc travel bursaries

2007-06-26 Thread Jim Pflugrath
I just wanted to re-post this in case you know someone who wants some travel money. Jim Rigaku Americas Corporation is pleased to announce the availability of five (5) awards of $500 each to post-doctoral research fellows to help with the costs of travel to upcoming summer meetings such as

Re: [ccp4bb] Help with reducing crystal mosaicity

2007-07-09 Thread Jim Pflugrath
What is the mosaicity of the unfrozen crystal? Jim -Original Message- From: Mary Fitzgerald [EMAIL PROTECTED] Date: Mon, 9 Jul 2007 18:05:10 To:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Help with reducing crystal mosaicity Help please! I'm looking for some new ideas. I have

Re: [ccp4bb] ccp4 pack_images program?

2007-08-23 Thread Jim Pflugrath
Is there any advantage to bzip2-ing the individual images rather than making one bzip2-ed tarball with tar cvfj? Yes. If you have folks sending you images by sftp or e-mail, then you don't have ensure a tarball of Giga or Tera bytes works. You can send the smaller multiple files and restart

Re: [ccp4bb] To bathe or not to bathe.

2007-11-23 Thread Jim Pflugrath
It probably goes back to the days of using a single-counter diffractometer where one didn't have multiple Bragg reflections on an image or film pack. That is, each reflection was collected by itself. Even in a small molecule crystal data collection nowadays, it would not hurt to have the crystal

[ccp4bb] Scientist / Programmer position available

2007-11-26 Thread Jim Pflugrath
Folks, I wanted to call your attention to the following position(s) available at Rigaku. Thanks, Jim Scientist/Programmer Rigaku, the world's largest analytical X-ray company, is seeking experienced scientific programmers to join well-recognized Rigaku scientists such as Jim Pflugrath

Re: [ccp4bb] ideal bond length and bong angel

2008-01-09 Thread Jim Pflugrath
Bong angels are probably ideal already! Please explain, so that I can teach this to my students. :) Jim

Re: [ccp4bb] Malic Acid interferes heavy metal binding?

2008-01-14 Thread Jim Pflugrath
Did you grow Malic Acid crystals? I see no reason why glycerol cannot be the precipitant. I am aware that at least one protein is crystallized with ethylene glycol as the precipitant. On Wed, 9 Jan 2008, JINJIN ZHANG wrote: Dear All, I have got large and nice crystals in a condition

Re: [ccp4bb] indexing multiple lattices

2008-02-18 Thread Jim Pflugrath
Is there any way to do a search of crystal orientation matrices with a known cell to find the best fit to the diffraction pattern? The data were collected on the Pilatus6M detector so I am limited to mosflm and XDS for processing. d*TREK will easily process Pilatus6M images. Both packages

Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth

2008-02-27 Thread Jim Pflugrath
There are many excellent review articles about cryocrystallography and cryoprotectants. Do labs generally have these articles handy in a methods folder? Do lab heads help their colleagues by making them read them? Mineral oil is generally not a good oil to use because it changes volume too

Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth

2008-02-27 Thread Jim Pflugrath
Hi everyone, I received a lot of positive e-mails about my post on cryo methods. One theme was, Well, what are the papers I should read? Blatant self-promotion I know of one such paper published in Methods. I have made the PDF of it downloadable from our web site at

Re: [ccp4bb] question about processing data

2008-03-17 Thread Jim Pflugrath
I would use all the data myself and report that the model was built from a a dataset with 74% completeness in the 2.25 to 2.15 Anngstrom shell. I would not put the number 2.15 A in the manuscript title nor in the poster title. For me the acceptable completeness is 90% in the highest

Re: [ccp4bb] Are Calcium Citrate Crystals A Common False Positive?

2008-04-29 Thread Jim Pflugrath
That's an easy hypothesis to test. Simply set up your drops with the same conditions except without protein and see if you get crystals. Please let us know the results. Thanks! Jim On Tue, 29 Apr 2008, Sam Stephenson wrote: Are calcium citrate crystals a common false positive in trays

[ccp4bb] 2008 Rigaku Post-doc Summer Travel Bursary Awards (fwd)

2008-05-04 Thread Jim Pflugrath
(CST) From: Jim Pflugrath [EMAIL PROTECTED] Subject: 2008 Rigaku Post-doc Summer Travel Bursary Awards Rigaku Americas Corporation is pleased to announce the availability of five (5) awards of $500 each to post-doctoral research fellows to help with the costs of travel to upcoming summer meetings

Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein

2008-05-27 Thread Jim Pflugrath
Have you thought about phasing off the sulfurs? This is quite a common technique nowadays. Jim On Tue, 27 May 2008, Joe Smith wrote: Dear all, Sorry for an off-topic query. I have been unable to crystallize a Se-met containing protein (8 Met in 206 amino acids) in the native crystallization

[ccp4bb] cryo-cooling, was: Re: [ccp4bb] crystallisation and mosaicity

2008-06-06 Thread Jim Pflugrath
I would like to point out that flash-cooling in liquid propane has the added complication that the liquid propane can have a range of temperature and still be liquid. If you use propane you may not know which temperature you are actually using. The temperature in the exposed layer of the

[ccp4bb] Course: CSHL 2008 X-ray Methods in Structural Biology

2008-06-10 Thread Jim Pflugrath
Folks, sorry for the belated announcement, but I noticed the application deadline is creeping up on us. Jim X-ray Methods in Structural Biology Cold Spring Harbor Laboratory October 13th-28th, 2008 Deadline for applications: June 15th This

Re: [ccp4bb] alternatives to IZIT

2008-06-16 Thread Jim Pflugrath
Whatever dye(s) you use, be sure to run some positive and negative controls to see how the dye really works. Jim On Sat, 14 Jun 2008, Mark Del Campo wrote: Before I place an order for some Izit, are there some other dyes I can use to check if I've got a protein crystal? Thanks, Mark

Re: [ccp4bb] is it Ok to freeze

2008-06-19 Thread Jim Pflugrath
I've been in that cold room / hutch. I never heard of it being flushed with LN2. I think that is just to make the room sound cooler. Jim On Thu, 19 Jun 2008, Mischa Machius wrote: Sadly, I have never seen the room being used. Perhaps one of the 'older' Martinsrieder on the forum has seen

Re: [ccp4bb] Are cell parameter shifts real?

2008-09-09 Thread Jim Pflugrath
How would you tell the difference between a unit cell shift and a wavelength shift when collecting diffraction data at a synchrotron beamline? Well, all the cell length would scale by the wavelength, so that would be one hint that the wavelength changed. If a got longer and c got shorter, then

Re: [ccp4bb] disulfide bonds, SE sample, and Xray absorption edges

2008-09-25 Thread Jim Pflugrath
There is ALWAYS anomalous scattering. You do not have be at the absorption edge to get it. The question is just whether your experiment is good enough to detect it. So your question of overlapping always has the answer Yes, but I would remove the words absorption edge from your question.

Re: [ccp4bb] foam dewar usage ?

2008-10-09 Thread Jim Pflugrath
A good cover -- judiciously used -- goes a very long way in reducing ice in dewars whether the dewar is made of foam, glass or stainless steel. If you keep your dewar covered with a lid that extends on the outside of the dewar down a few centimeters below the dewar edge, you will have minimal

Re: [ccp4bb] About system absence in P4222?

2008-12-15 Thread Jim Pflugrath
Ian, are you saying that one might need to know some crystallographic theory in order to determine space groups? Or can we simply click a few buttons in a graphical user interface and be done with it? Jim On Mon, 15 Dec 2008, Ian Tickle wrote: But that only means that the SF contribution

Re: [ccp4bb] structure (factor) amplitude

2009-01-12 Thread Jim Pflugrath
I wonder if the early use of the shortened structure amplitude is because it was a pain to do any typing, word processing, typesetting, etc before Gutenberg. But soon crystallographers will be solving all their structures on their cell phones and also just text messaging manuscripts to

Re: [ccp4bb] sticky crystals

2009-01-27 Thread Jim Pflugrath
Put a small piece of dry ice on the opposite side of the plastic from the crystal. Perhaps the difference in thermal expansive coefficient will let the crystal(s) break away. Don't overdo it though. This is a trick that Gary Gilliland taught me. Jim On Wed, 28 Jan 2009, Savvas Savvides

Re: [ccp4bb] Problems with phasing a protein (1300aa)

2009-03-20 Thread Jim Pflugrath
Well, what do you expect the anomalous signal contributed from your 45 seleniums in a perfect world to be when the asymmetric unit contains 1300 aa? Do you think a dataset with Rmerge of ~15% is good enough to detect a signal of even 2%? (Note: I did not do the calculation, so I just made up

Re: [ccp4bb] Problems with phasing a protein (1300aa)

2009-03-23 Thread Jim Pflugrath
On Mon, 23 Mar 2009, Phil Evans wrote: I'm happy to change the column titles if it makes it clearer. Actually the I/sigma column in the Scala output is not very useful: it is I / RMSscatter, ie the mean intensity/mean error, for individual observations, not taking into account multiple

Re: [ccp4bb] Problems with phasing a protein (1300aa)

2009-03-24 Thread Jim Pflugrath
Hi Tassos, It's a bit early in the year to have our annual I/sigI discussion on the CCP4BB, isn't it? Usually, we wait until at least April 1. :-) . d*TREK could confuse people further as to which one should be used for reporting and decision making. . The Big Question Again:

Re: [ccp4bb] Crystal vacuum cleaner

2009-03-26 Thread Jim Pflugrath
If I understand you correctly, you are writing about sucking a crystal up into a small capillary. This is an ancient technique used with the very first protein crystal diffraction data collection in the 1950s and 1960s that is still used today. You can use a small 1 ml plastic syringe for the

Re: [ccp4bb] I/sigma continued

2009-03-30 Thread Jim Pflugrath
That leaves the question of how to label these statistics in a consistent, clear and concise way: suggestions? Phil Evans Here is a suggestion. :) FWIW, dtscaleaverage labels the mean I/sigmaI of the individual input reflections as I/sig unavg. That is, before any averaging is performed.

Re: [ccp4bb] cryoprotectant for 1,6 hexanediol

2009-04-02 Thread Jim Pflugrath
The cryoprotectant is 1,6 hexanediol. Jim On Thu, 2 Apr 2009, HanJie_Heng Chiat Tai wrote: Hi, I have a crystal grown in 2.1M 1,6 hexanediol/0.1 M tro-sodium citrate (pH 6.5). What's the cryoprotectant can be used to flash cool this crystal? Any online protein crystal

Re: [ccp4bb] Another scaling question

2010-06-24 Thread Jim Pflugrath
It might be instructive to draw a precession-like diagram of your reflections in reciprocal space. Remember that reciprocal space dimensions are generally in reciprocal Angstrom and volumes raise those dimensions to the third power. Thus (1/12)^3 to (1/15)^3 is not a big volume. How many

Re: [ccp4bb] Crystallization of low solubility proteins from glycerol-containing solutions

2010-08-25 Thread Jim Pflugrath
Have you tried to use glycerol or ethylene glycol as the precipitant? What happens when you go to 50% or higher concentrations? _ From: CCP4 bulletin board [] On Behalf Of Roger Rowlett Sent: Wednesday, August 25, 2010 9:19 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules

2010-09-09 Thread Jim Pflugrath
This cryocrystallography webinar lists some common cryoprotectants: -Original Message- From: CCP4 bulletin board [] On Behalf Of Chris Weichenberger Sent: Thursday, September 09, 2010 7:34 PM To:

Re: [ccp4bb] Is the Rmerge invalidate by twinned data?

2010-10-06 Thread Jim Pflugrath
It may be time for our annual I/sigmaI discussion. Please note that I/sigmaI is what the RCSB expects from you and it is generally lower than I/sigmaI. Some packages do not output I/sigmaI in an obvious place for you to put in your Table 1. :) On Wed, 6 Oct 2010, Ed Pozharski wrote: You

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

2010-10-28 Thread Jim Pflugrath
Zbyszek, Since you mention I/sigmaI in your PDF, do you mean I/sigmaI or I/sigmaI? Do you mean I/sigmaI (in whatever rendition you choose) for the averaged unique reflections or the I/sigmaI for the observations? Also since one can adjust sigmaI in your scalepack program through the use of the

Re: [ccp4bb] Strange spots

2010-10-29 Thread Jim Pflugrath
Are these very strong reflections? Do they appear on more than one image? Are they an artefact of the detector or the image display program?

Re: [ccp4bb] Crystal gel band

2010-11-02 Thread Jim Pflugrath
It reads like you need to run a lane or two with a positive control of some kind. Can you grow lysozyme, glucose isomerase, hemoglobin or other crystals of a protein around the same expected molecular weight and try run on the gel lanes with about the same amount of crystalline volume as your

Re: [ccp4bb] High Rmerge with thin frames

2010-11-05 Thread Jim Pflugrath
In general, if the Rmeas or Rmerge is high in the low resolution shells, then something is not optimal with the data collection. Bill Shepard has already mentioned the loop vibrating or moving in the cryogenic gas flow. Other problems could be the goniometer head was loose, the magnet was loose,

Re: [ccp4bb] how to optimize small rod-shaped crystals

2010-11-16 Thread Jim Pflugrath
With Izit or other dyes, you might wish to do a positive control with bona fide protein crystals and a negative control with bona fide salt crystals. _ From: CCP4 bulletin board [] On Behalf Of Matthew Bratkowski Sent: Tuesday, November 16, 2010 7:58 PM To:

Re: [ccp4bb] Heavy atom salt at low pH

2010-11-17 Thread Jim Pflugrath
Crystals of tendamistat were grown from hydrochloric acid and solved by MIR. I do not recall anything special about the heavy atom soaks, so try everything in your heavy atom closet. What have you tried that has not worked? _ From: CCP4 bulletin board [] On

Re: [ccp4bb] Merging data to increase multiplicity

2011-01-28 Thread Jim Pflugrath
You should know that your crystal mosaicity is a physical property of your crystals and the diffraction experiment. Generally, it is anisotropic though most programs output a single value. How can that single value describe what is really happening in your experimental data? You can do

Re: [ccp4bb] Detaching crystals from glass cover slides

2011-02-09 Thread Jim Pflugrath
Cool the coverslip on the opposite side of the crystal with a chip of dry ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I wonder if you can simply move the whole tray into a cooler temperature? You can imagine that the thermal expansion coefficient of the glass

Re: [ccp4bb] while on the subject of stereo

2011-03-01 Thread Jim Pflugrath
I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-03 Thread Jim Pflugrath
As mentioned there is no I/sigmaI rule. Also you need to specify (and correctly calculate) I/sigmaI and not I/sigmaI. A review of similar articles in the same journal will show what is typical for the journal. I think you will find that the I/sigmaI cutoff varies. This information can be used

Re: [ccp4bb] glycerol

2011-03-10 Thread Jim Pflugrath
Glycerol is just another additive to crystallizations and a reasonably good cryoprotectant. Sometimes it helps to grow crystals, sometimes it has no effect, and sometimes it interferes with crystal growth. Have I covered all the possiblities? One thing is the glycerol often makes a protein

Re: [ccp4bb] metal binds?

2011-03-25 Thread Jim Pflugrath
Collect all your diffraction data in your home lab, solve the phase problem, fit the map, refine, deposit coordinates in the PDB. _ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Careina Edgooms Sent: Friday, March 25, 2011 2:40 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Reproducing crystals.

2011-04-12 Thread Jim Pflugrath
Frances Jurnak published a paper in 1986 on PEG impurities and purification. As I recall, it turns out that different manufacturers put different additives in PEGs as preservatives. These are generally anti-oxidants. PEGs do get oxidized. I suggest you heat up your new PEG solutions to say 80

[ccp4bb] 250 years of Bayes' Theorem: Link

2011-04-20 Thread Jim Pflugrath
This link should be helpful to many folks here:

Re: [ccp4bb] Difficulty indexing diffraction, cell too small

2011-05-17 Thread Jim Pflugrath
In general, the Rmerge and Rmeas should get better with a lower symmetry spacegroup, so that's weird. Maybe you didn't crystallize what you thought you crystallized. Do people runs gels anymore on crystals to get an idea of what's in the crystal or do they do MassSpec? I think another way to go

Re: [ccp4bb] Difficulty indexing diffraction, cell too small

2011-05-18 Thread Jim Pflugrath
Yes, reciprocal lattice coordinates are available for reflections with d*TREK. My colleague has also written a reciprocal lattice viewer which takes image pixels and transforms them to a reciprocal lattice. I'm sure others have similar programs. But in this modern internet age, I would say

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