[ccp4bb] twinning or not?

Hello, I have run into a very odd situation. Upon collection and data processing on a crystal on my home source all pointers seemed to show twinning. Was not surprised since previous crystals under different but related conditions have showed significant twinning though the cell dimensions

Re: [ccp4bb] High Temperature Factors with TLS

t; On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. mailto:lmtho...@ou.edu>> wrote: Hello All, A general questions though phenix.refine is being used for refinement. A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters. They

[ccp4bb] High Temperature Factors with TLS

Hello All, A general questions though phenix.refine is being used for refinement. A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters. They were given the structure to gain some experience in refinement and they have been asking me

[ccp4bb] shipping dewar question

Hello All, I have had an odd thing happen with one of our CX100 shipping dewars. It became obvious that it had lost its vacuum, cold outside, LN2 boiling off quickly. I pumped the dewar down, vacuum was not great but I figured I would test to see if it was holding vs. warming up immediately.

Re: [ccp4bb] Odd Positive Density Around a Cystine

sult. > > The only other way to end up with a parameter that directly conflicts with > the difference density is a bad restraint, but that doesn't sound likely > based on your description. > > Dale Tronrud > > On 8/10/2022 7:59 AM, Thomas, Leonard M. wrote: >>

Re: [ccp4bb] Odd Positive Density Around a Cystine

ucture. Roger Rowlett Gordon & Dorothy Kljne Professor, Emeritus Department of Chemistry Colgate University On Wed, Aug 10, 2022, 11:00 AM Thomas, Leonard M. mailto:lmtho...@ou.edu>> wrote: Hello All, I have run into something odd. In working on a structure for one of the groups I wor

[ccp4bb] Odd Positive Density Around a Cystine

Hello All, I have run into something odd. In working on a structure for one of the groups I work with regularly, on one of the cystine residues I have a very large positive density peak at the sulfur position. The B value is approximately 4 times the other values in the residue and on other

[ccp4bb] oily material at cold stream tip

So here is a new one, I seem to have an oily substance at the end of our Oxford Cryostream. It is greenish in color and I honestly have no idea where it may be originating from. The tubes leading into the head look clean. I first noticed it on the paddle I use to block it when mounting

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

After taking images at room temp and assuming good diffraction then, I would kick up the PEG400 concentration and as a first go on the PEG400 condition and try low molecular weight PEG's as a cryo protectant for the other two conditions. Good Luck, been there and have exposed many crystals in

Re: [ccp4bb] Rigaku CrystalTrak Web not working

So I just checked ours and you should be able to access the interface unless your institution is blocking it. You can not look at individual drops but if you go to the XXL in the Thumb drop down then you can at least see if anything maybe in the drops. And as mentioned looking locally is

[ccp4bb] neg density/high B on sidechains

Hello all, This is one of those issues that seems to come up now and then. I have been working on a structure that obviously has some radiation damage as indicted by negative density and/or high thermal parameters. Since we know that residue X is in the sequence the sidechain should be there

[ccp4bb] Postdoctoral position at the University of Oklahoma

I am posting this a faculty member here. Please address any questions to her. Postdoctoral position available immediately in Singh Group at OU. Biochemist or Structural Biologist: Seeking a highly motivated postdoc with experience in one or more biochemical techniques involving cloning, protein

[ccp4bb] TEM Position

Hello All, Attached is a posting for a Staff Scientist position here at the University of Oklahoma. Please direct all questions and inquires to the contract information in the ad. Leonard Thomas lmtho...@ou.edu

[ccp4bb] Post-doc Univeristy of Oklahoma-Norman

I am posting this for Shanteri Singh a faculty member here at OU. Please direct any questions to her. Postdoctoral position available immediately in Singh Group at OU. Biochemist or Structural Biologist: Seeking a highly motivated postdoc with experience in one or more biochemical techniques

Re: [ccp4bb] suggestions for cryoprotectant

This is the first thing you need to do before going down the rabbit hole looking for a cryo protectant. Mitegen make it much easier then in the 'old days' of capillaries. Good luck, Len lmtho...@ou.edu On Oct 20, 2018 2:02 AM, Andreas Förster wrote: Dear Firdous, get some Mitegen sleeves

[ccp4bb] cif questions

Hello All, We have run into a problem recently when working with cif files for ligands that have been either soaked or cocrystallized with the proteins we are looking at. Most of the ligands cif files have been used previously and while not in the CCP4 library database are available from the

Re: [ccp4bb] Do you have this type of diffraction pattern?

Looking a bit closer are you sure the crystal is protein? I see a couple of spots which could indicate a small molecule of some variety. Len On Nov 30, 2017, at 3:04 PM, Geny > wrote: ​ Dear EveryOne, ​ ​ I recently tried to collect the diffraction

Re: [ccp4bb] sending dewar to synchrotrons

on this? E.g, what carrier? What synchrotron? And who returns them—the carrier? We just sent a dewar to APS via FedEx last week, and we had no problems (other than the fact that FedEx didn’t come to pick it up until 7:30 PM…) Cheers, Pat Loll On 20 Nov 2017, at 3:14 PM, Thomas, Leonard M. <

[ccp4bb] sending dewar to synchrotrons

Hello All, General inquiry here, I have been sending dewars out to synchrotrons for many years now and all of a sudden we have run into them being returned due to incomplete paper work or hazardous problems. I was just wondering if anyone else had had this happen in the past and what you may

Re: [ccp4bb] Crystal with ZERO diffraction

Just my 2 cents worth, I am with others in that this is actually not unusual. Outside of what Patrick said the first thing to look at if you can is does the crystal diffract at all. You can do this by taking a room temperature shot, the Mitegen loop/sleeve/pins work well for a quick shot or

Re: [ccp4bb] {meta} posts with pdfs

Overall this board is relatively spam/scam free. I think most users can figure out what is a legitimate post vs. something malicious. I doubt restricting post with pdf attachments will make a big difference. There was a time when any attachment was discouraged but that seems to have fallen

Re: [ccp4bb] RapiData at SSRL 2017

101 Stephenson Parkway Norman, OK 73019 405-325-1126 lmtho...@ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Thomas, Leonard M. <lmtho...@ou.edu> Sent: Wednesd

Re: [ccp4bb] RapiData at SSRL 2017

Hi Clyde, We have a crystal collecting now. If it does not finish by the time our time is up you can remove it. It is sort of a lets take some frames and see if we can do anything with it. Overall the run was okay, ended up with some useful information, not sure about publishable data but we

[ccp4bb] OSX or Linux system?

Discussion on what runs/does not run under windows has moved me to asked is there a somewhat preferred platform of Linux vs. OSX. I am replacing an 8 year old Mac Pro, big silver box, as it really is slowing down comparatively speaking and 8 years is a good run for a computer and it will get

Re: [ccp4bb] strange X-ray diffraction diagram——RNA Or Complex？

Yujie, I would try using another processing program if you have it available, say Mosflm. I look at similar looking diffraction data recently, though without the salt crystals mixed in as Herman observed which you also need to take care of in the future, and HKL did not handle if very well,

[ccp4bb] handling crystals in volatile solvents

Hi All, We have gotten some very nicely formed crystals out of a couple of different volatile solvents recently. Besides looking for something easier to work in does anybody have any tips on handling crystals from these types of solvents. It is very hard to loop a crystal while it is doing

[ccp4bb] Peltier cooled incubators

Little off topic and after a quick search I could not find much on the BB already. We are looking at purchasing a larger Peltier cooled incubator for crystal trays. They are designed to go down to 15 C. I know people have had pretty good luck with the bench top models but we are looking at a

Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

My guess you might just have to reinstall with the latest version of nedit. That is what I had to do when I went from 10.5 to 10.9. Have yet to jump to 10.10 yet. Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and

[ccp4bb] Post Doctoral Position - University of Oklahoma

The following position is available at the University of Oklahoma. Please contact Liz Karr for any addition information. A Postdoc position is available in microbiology and structural biology in the research group of Dr. Liz Karr in the Department of Microbiology and Plant Biology at the

[ccp4bb] Post Doc Postion in Oklahoma

I am posting this position announcement on the behalf of Dr. Rakhi Rajan, please direct any questions to her. A Post-doctoral Research position is available in the laboratory of Dr. Rakhi Rajan in the Department of Chemistry and Biochemistry at the University of Oklahoma. The research is

[ccp4bb] Assistant Professor – Structural Biology/Natural Products-U of Oklahoma

Faculty position open at the University of Oklahoma. Assistant Professor – Structural Biology/Natural Products. The Department of Chemistry and Biochemistry (http://chem.ou.edu) at the University of Oklahoma invites applications for a tenure-track faculty position at the rank of Assistant

Re: [ccp4bb] emergency substitute for RT loop cover?

Paratone might work. It is thick enough to hold the crystal in place I would think. Small molecule crystallographers use to use it all the time at both room temperature and cryo temperatures. Len Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma

Re: [ccp4bb] Room temperature data collection

To add my 2 cents. Recently we have screened a lot of really poor looking crystals. We had tried originally at cryo temps and really were quite unsure as to weather they were protein, just poorly diffracting crystals, etc.. We then mounted some at room temperature and were able to observed