Re: [ccp4bb] Co-Crystallization with drug molecule

Hello Amit, In addition to what others have written, if you have some of your compound dry (not in DMSO), then adding this directly to your preformed crystals has worked for us on several occasions. In this instance, one would take a small/ fine pipette tip and dip this into your compound and t

Re: [ccp4bb] Crystal optimization

I believe someone has already mentioned matrix seeding- taking the crystals you currently have, making microseeds and then using this in a new screen (whatever your favourite initial screens may be). This can give you different conditions that will give you better crystals as you already have se

Re: [ccp4bb] Data Processing questions

Hello Marco, There are schools that will teach you about the software (and theory) used in crystallography and they tend to be very good, so one suggestion is to enroll in one of these 1-2 week courses to learn everything properly. You should process all of your data sets- it is only after havi

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

I agree with Harry, I suspect that embarrassment has no definition/ meaning in the context of Nature. From: CCP4 bulletin board on behalf of Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> Sent: Tuesday, May 14, 2024 6:28 PM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Ubuntu and Coot

bulletin board on behalf of Tom Peat <b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, May 9, 2024 9:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ubuntu and Coot You don't often get email from b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk. Learn why this is impo

Re: [ccp4bb] Ubuntu and Coot

on my computer. I did not have any issues with Coot even in CCP4 8.0.017. I am sorry I don't know the reason of the error... Cheers, Martin On 08/05/2024 06:59, Tom Peat wrote: Hello All, I'm not sure if this is specific to me or whether I missed the fix, but I'm currently runnin

[ccp4bb] Ubuntu and Coot

Hello All, I'm not sure if this is specific to me or whether I missed the fix, but I'm currently running Ubuntu 22.04.1 and updated to the latest ccp4 version 8.0.019 and Coot crashes. I tested to see whether it was just the ccp4 version by downloading coot separately into my bin directory (co

Re: [ccp4bb] Crystallographic data table

Hello Marco, You can find all of that information in the Aimless log file. Best regards, Tom Get Outlook for iOS From: CCP4 bulletin board on behalf of Marco Sent: Monday, April 1, 2024 2:40:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4

Re: [ccp4bb] Difficult Molecular replacement

Hello Marco, This may seem a little obvious, but did you check the sequence of your protein from the gel/ crystals? I've found mass spec to be very useful in this regard as we've had at least two instances of having a protein that looked to be the right size/ correct protein, but wasn't after m

Re: [ccp4bb] Automated refinement convergence

That is an interesting point, for those using big clusters to do extensive computing work. I assume universities are 'going green' but that it will take a while for this to happen. I just use my home computer and have my own solar panels and battery to keep things running. cheers, tom _

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

han 3 for our glycol refinement. How much less is related to the restraint weight we set in Refinement. Cheers, Robbie On 6 Jan 2024 23:26, Tom Peat mailto:t.p...@unsw.edu.au>> wrote: Hello Robbie, Thanks for the stats and description of what has been done. I think this puts us back into th

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

ot as intellectually gratifying as having a cut and dry answer to these questions that come up rather frequently. Thanks again for the stats and description. cheers, tom From: Robbie Joosten Sent: Sunday, January 7, 2024 8:24 AM To: Tom Peat ; CCP4BB@JISCMAI

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

It appears that Zhonghao might be worried about his data to parameter ratio. At 3 A, one can easily be in a situation where one has fewer reflections than four times the number of atoms (X, Y, Z plus B). I like the idea of starting out with the average B (or even Wilson B) and then doing TLS as

Re: [ccp4bb] Query on density fitting to phosphate

, tom From: Dale Tronrud Sent: Monday, December 25, 2023 8:52 PM To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Query on density fitting to phosphate [You don't often get email from de...@daletronrud.com. Learn why this is important at http

Re: [ccp4bb] what is isomorphous?

Hello All, I think Randy makes a very good point here- it depends on what you are trying to do with your data sets. If you are trying to merge them, 'isomorphous' is important for this to work. If you are using them for cross crystal averaging, being less isomorphous is better (more signal). J

Re: [ccp4bb] Query on density fitting to phosphate

Hello Arpita, If you look up the f" values of various elements ( http://www.bmsc.washington.edu/ ) you will see that there are elements which will give you more or less signal at your wavelength of 1.5412 eV. For example, phosphate can be seen to have an f" value of about 0.43 e at that wavelen

Re: [ccp4bb] Query on density fitting to phosphate

Dear Arpita, The hydrogens on phosphate, just like sodium and potassium, will come off the oxygens in water. To be more explicit, you don't have mono- or di-hydrogen phosphate in water (except transiently), you just have phosphate, depending somewhat on the pH of course. At 2.5 Angstrom resolut

Re: [ccp4bb] Coot query

Just in case something like this happens to someone else: I am running the Gnome display server and I did another restart and I can now run Coot. The magic of rebooting... cheers, tom From: Paul Emsley Sent: Friday, July 7, 2023 2:09 AM To: Tom Peat ; CCP4BB

[ccp4bb] Coot query

Hello All, I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy 7.81.0) and tried to start up Coot and received the following error message: The program 'coot-bin' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue (

[ccp4bb] Just a reminder

.org/ cheers, tom Tom Peat, PhD one of many on the committee... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issue

Re: [ccp4bb] To Trim or Not to To Trim

est regards, Debanu -- Debanu Das, https://bio.site/debanu_das On Fri, Mar 10, 2023 at 12:41 PM Tom Peat mailto:t.p...@unsw.edu.au>> wrote: Hello All, I agree with Dale that we don't have a good way to model these things and it has been a discussion for a very long time with no proper ans

Re: [ccp4bb] To Trim or Not to To Trim

Hello All, I agree with Dale that we don't have a good way to model these things and it has been a discussion for a very long time with no proper answer. Two more small points- we (or at least I do this all the time) don't model the N- or C-terminal residues that I don't see. They are most like

[ccp4bb] a reminder

://www.iucr.org/iucr/cong/2023-iucr-xxvi https://iucr2023.org/ cheers, tom Tom Peat, PhD one of many on the committee... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA

[ccp4bb] Just a reminder

/ cheers, tom Tom Peat, PhD one of many on the committee... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to mem

Re: [ccp4bb] Interesting Density

I second glycerol. Best regards, tom Get Outlook for iOS From: CCP4 bulletin board on behalf of kotping Sent: Tuesday, December 6, 2022 6:02:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Interesting Density You don't often get em

[ccp4bb] IUCr in 2023

Hello All, Some of you may have noticed that the deadline for abstract submission for the IUCr meeting in Melbourne, Australia passed just recently. There are reasons for the early deadline, but please forgive us for that. There is an extension/ second call for abstracts which will be advertise

Re: [ccp4bb] Lower b-factors with increasing T

I think the basic question being asked is why are the B-factors going the 'wrong' way? That is, as the temperature increases, one might expect higher B-factors (at least that is what we are taught) whereas what Matt is seeing is the opposite- decreasing B-factors as one goes up in temperature (w

[ccp4bb] coot crashing

Hello All, Just wondering if anyone else is having issues with Coot crashing (regularly, not just once in a while). I get the following error message: /home/pea246/bin/ccp4-7.0/bin/coot: line 318: 2025 Segmentation fault (core dumped) $coot_bin "$@" guile (GNU Guile) 2.2.3 Packaged by

Re: [ccp4bb] Non-Cysteine modification with heavy atom

Hello Chandra, Soaking heavy atoms into crystals has a long and successful history (I use it pretty often and it works much of the time). If you need phase information and you have some crystals, I would certainly give it a try. There are many papers and books to give you methods to do this (go

Re: [ccp4bb] Assumptions on protein activity (again)

other than the one 'optimal' condition. Best regards, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board on behalf of Markus

Re: [ccp4bb] Protein is dimmer in solution, hard to build two chains in crystal structure

, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board on behalf of Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent:

Re: [ccp4bb] crystals that dont diffract :( :(

?We have some crystals that diffract well when fresh (less than one week old) but lose almost all diffraction by the end of 2 weeks, so age can matter. One crystals are in liquid nitrogen, they should be safe from further degradation, but may suffer from ice contamination. cheers, tom Tom

Re: [ccp4bb] Acceptable range of CC1/2

I think all of those numbers would be pretty acceptable to almost all referees ;-) Cheers, tom From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Deepali Verma Sent: Tuesday, 5 June 2018 7:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Acceptable range of CC1/2 Dear all, I

Re: [ccp4bb] suggestion of crystallization optimization

ature? Best of luck, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board on behalf of Liuqing Chen <519198...@163.com> Sent: Mon

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

Unfortunately it is unlikely that the costs for robotic equipment (at least the larger scale equipment) will come down much. It is effectively all ‘bespoke’ equipment and will never benefit from high volume manufacturing (nothing like phones or cars). How many crystallisation centres are needed a

Re: [ccp4bb] new ContaMiner features

I agree with Tristan, it can be quite easy to crystallise a contaminant even when one is trying to be careful during the purification process. Before everyone had a mass spec, looking at gels didn't tell you as much as you needed to know, as many proteins don't stain well, so are hard to see on

Re: [ccp4bb] Large scale mammalian expression system recommendation?

Hello All, I would second the notion that transient systems are quite good for testing expression levels on the small scale and can be used for scale up (to a certain degree at least). It is probably the fastest way to go to screen a number of constructs. Cheers, tom -Original Message--

Re: [ccp4bb] Primer design

A lot of plant genomes are big- wheat for example is 12 Gb, so it may not be quite as trivial as one might expect. cheers, tom Tom Peat Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au

[ccp4bb] postdoctoral position available

Dear Board Readers, For anyone who might be interested, or know of interested persons, there is a postdoctoral position available at CSIRO: https://career10.successfactors.com/sfcareer/jobreqcareer?jobId=39270&company=CSIRO&username Best regards, tom

Re: [ccp4bb] intermolecular dissulphides

ect on the stability of the protein. ?We also saw this was consistent across multiple space groups. If you would like to have a look, they were just released: 5HY0, 5HY2, 5HY4. As a comparison to another protein in this fold class that doesn't have the disulfide is 5HWE. cheers, tom To

Re: [ccp4bb] just out of totally idle curiosity ...

I don't know about Europe, but it is very tight Down Under... -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William G. Scott Sent: Wednesday, 9 November 2016 4:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] just out of totally idle curiosity

Re: [ccp4bb] Interesting DNA contamination

I think the more interesting questions are: should one want to disrupt such a tight interaction? Wouldn’t the structure of the protein bound to DNA be more interesting than the protein alone? Why not try to crystallize the complex and show how the protein binds? Sometimes you should just run with

Re: [ccp4bb] [RANT] Reject Papers describing non-open source software

port their software after others have gone in and modified it, which is unrealistic. I just think it is unrealistic to expect the source code just because someone wrote a paper (again, I like open source, but not everything is destined to be open source). cheers, tom Tom Peat Proteins Group

Re: [ccp4bb] crystallographic confusion

cularly in the process of reviewing papers). cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Willia

Re: [ccp4bb] question on charge charge interactions

in either case but more so for acidic residues. See HIV protease Asp-Asp as a well-established example Hope this helps J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Friday, 28 March 2014 12:12 p.m. To: CCP4BB@JISCMAIL.AC.UK S

[ccp4bb] question on charge charge interactions

Hello All, I am appealing to the community as I don't seem to be able to find through Google what I am looking for, and I just don't have the ability to look through every structure in the PDB to find this. I have what I think is an interesting case: a two domain protein structure with a most

Re: [ccp4bb] Biacore/SPR

throughput). Good luck, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bosch, Juergen [jubo...@jhsph.edu] Sent: Tuesday

Re: [ccp4bb] questions

vourable, allowed /poor and outliers) in the table, so the editor clearly wants something different. When I took a guess by putting in the 'MolProbity score' I was basically called an idiot that can't follow directions. Help on this front would be appreciated as although I hav

Re: [ccp4bb] statistical or systematic? bias or noise?

Slightly off the topic, but still potentially relevant in terms of realistic experimental error: when dealing with the small volumes typically used in crystallization (say 1 uL + 1 uL drops), and using a 10 uL pipette, the errors are fairly high (more like 30% than 5-10%), leading to a lot of n

Re: [ccp4bb] archival memory?

A chip in my brain to remember all of the things I should know/remember would be very convenient if we are really talking about having a good memory system. It means it would also be easier to extract that personal perspective and pass it on. Cheers, tom From: CCP4 bulletin board [mailto:CCP4B

Re: [ccp4bb] Reservoir buffer

The following could be of use: Newman, J. Expanding screening space through the use of alternative reservoirs in vapor diffusion (2005) Acta Cryst D61(4), 490-493 Cheers, tom From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Tuesday, 13 November 2012 5:17

Re: [ccp4bb] Who is using 64-bit Linux?

notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: > We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work > fine on this. > I can't say I notice a big performance boost from the 64 bit side of things. > Maybe I'm just impatient. >

Re: [ccp4bb] very informative - Trends in Data Fabrication

(at least in many ways). I would be happy to give my name when reviewing, as I feel it is my job to improve the paper, and I can still face my colleagues after the exercise. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419

Re: [ccp4bb] Who is using 64-bit Linux?

We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052

Re: [ccp4bb] very informative - Trends in Data Fabrication

Bernard went to a lot of work to verify that this structure was wrong, so we should also thank him for his efforts. It is good to see someone who has a hunch follow that up and let the rest of us know about it. Thanks Bernard! Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville

Re: [ccp4bb] pH optimisation for crystallisation

If you find yourself in the situation where the buffer you started with is out of range of the pH you would like to attain, there are sets of buffers you can use that contain most of the standard buffers that will give you a fairly linear response across ~4-10, as described by Newman, Acta Crys

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

To elaborate further on software packages available that do a reasonable job of fitting small molecules and outputting reasonable dictionaries, one could consider Afitt from OpenEye Scientific Software. They have academic as well as commercial licenses to their software. Cheers, tom -Orig

Re: [ccp4bb] spherulites and PEG3350

You might to consider that PEG 3350 has phosphate contamination, so playing around with small amounts of phosphate (or removing it) might be worthwhile. Cheers, tom From: Regina Kettering [mailto:reginaketter...@yahoo.com] Sent: Thursday, August 25, 2011 04:46 AM To: CCP4BB@JISCMAIL.AC.UK Subjec

Re: [ccp4bb] CCP4 6.2.0 reading mtz files

Hello All, It turns out that the /tmp directory being used by ccp4i had incorrect permissions, which gave rise to the problem. Thanks for the solution! Cheers, tom -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Thursday, 21

[ccp4bb] CCP4 6.2.0 reading mtz files

I took a quick look via Google and in the FAQ to see if there was anything on this topic, but didn't find the clue I was looking for. I just installed version 6.2.0 on a linux box running Centos 5.6 and I get error messages every time I try to read in a mtz file- unreadable. I check the file us

Re: [ccp4bb] degradation of protein durring freez thaw

Hello again, I still think it depends on the protein complex, but I agree that the consensus/ hearsay/ anecdotal/ old crystallographer's tales revolve around complexes not working as well as single proteins for freezing. I'm not sure that has been shown to be the case, although again I would a

Re: [ccp4bb] degradation of protein durring freez thaw

Hello- Sorry to be disagreeable, but I think it depends on the protein. We've had much better success in getting reproducible crystals when we've snap frozen in liquid nitrogen in small aliquots (thin walled PCR tubes work best). We can then screen and optimize using the same protein prep- an

[ccp4bb] Crystallography position at CSIRO, Melbourne

://www.csiro.au/org/CMHT.html Questions can be directed to me (Tom Peat) at the following email address: tom.p...@csiro.au We seek an enthusiastic and highly motivated protein crystallographer to join the Structural Biology research group in Parkville. You will be responsible for protein

[ccp4bb] job avaiable

where Melbourne is...). cheers, tom Tom Peat CSIRO Molecular and Health Technologies 343 Royal Parade Parkville VIC 3052 Australia [EMAIL PROTECTED]