[ccp4bb] coot crashing

2019-07-11 Thread Tom Peat
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

2019-01-02 Thread Tom Peat
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

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

2018-10-12 Thread Tom Peat
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 Heckmann Sent

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

2018-08-20 Thread Tom Peat
, 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 :( :(

2018-08-14 Thread Tom Peat
?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

2018-06-05 Thread Tom Peat
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,

Re: [ccp4bb] suggestion of crystallization optimization

2018-06-04 Thread Tom Peat
? 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: Monday,

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

2018-04-26 Thread Tom Peat
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

Re: [ccp4bb] new ContaMiner features

2017-11-23 Thread Tom Peat
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?

2017-10-22 Thread Tom Peat
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

Re: [ccp4bb] Primer design

2017-07-24 Thread Tom Peat
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

2017-05-09 Thread Tom Peat
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=CSIRO Best regards, tom

Re: [ccp4bb] intermolecular dissulphides

2017-02-01 Thread Tom Peat
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 Tom Peat Proteins

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

2016-11-08 Thread Tom Peat
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

Re: [ccp4bb] Interesting DNA contamination

2015-06-25 Thread Tom Peat
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

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

2015-05-12 Thread Tom Peat
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 Biomedical

[ccp4bb] question on charge charge interactions

2014-03-27 Thread Tom Peat
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

Re: [ccp4bb] question on charge charge interactions

2014-03-27 Thread Tom Peat
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 Subject: [ccp4bb

Re: [ccp4bb] Biacore/SPR

2013-10-28 Thread Tom Peat
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

2013-10-17 Thread Tom Peat
. 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 have been called worse things, it would be nice to eventually get what is being referred to. Thanks, tom Tom Peat CSIRO

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

2013-03-13 Thread Tom Peat
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

Re: [ccp4bb] archival memory?

2012-12-12 Thread Tom Peat
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

Re: [ccp4bb] Reservoir buffer

2012-11-12 Thread Tom Peat
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

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

2012-04-04 Thread Tom Peat
this 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. cheers, tom Tom Peat

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

2012-04-03 Thread Tom Peat
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 +613 9662

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

2012-04-03 Thread Tom Peat
(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] very informative - Trends in Data Fabrication

2012-03-31 Thread Tom Peat
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

2012-02-08 Thread Tom Peat
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

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

2012-01-09 Thread Tom Peat
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

Re: [ccp4bb] spherulites and PEG3350

2011-08-24 Thread Tom Peat
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

[ccp4bb] CCP4 6.2.0 reading mtz files

2011-07-20 Thread Tom Peat
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

Re: [ccp4bb] CCP4 6.2.0 reading mtz files

2011-07-20 Thread Tom Peat
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

Re: [ccp4bb] degradation of protein durring freez thaw

2010-04-22 Thread Tom Peat
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-

Re: [ccp4bb] degradation of protein durring freez thaw

2010-04-22 Thread Tom Peat
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

[ccp4bb] Crystallography position at CSIRO, Melbourne

2009-12-09 Thread Tom Peat
://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