Re: [ccp4bb] muti-crystal averaging

As you say - HKL200 has a nomerge output. Pointless/Aimless can read such outputs and sort out any indexing alternatives, etc You can specify that the spacegroup should not change. (I presume this is not a major change? If your original SG is set to P1 and the program detects 222 symmetry the I

Re: [ccp4bb] challenges in structural biology

1.1  Getting many diverse conformations routinely into well-diffracting crystals;  and knowing how to interpret them biologically. On 15/07/2019 20:44, Holton, James M wrote: > Hello folks, > > I have the distinct honor of chairing the next Gordon Research > Conference on Diffraction Methods in

Re: [ccp4bb] challenges in structural biology

I like both of these points! I would comment/add the following: 1) What are the tools we can use for metals in structural biology? Note, I am biased here. -Including validation of solute ions like Na/K/Cl etc -Some metric of identity confidence? 2) Micro electron diffraction methods - ability

Re: [ccp4bb] muti-crystal averaging

Thanks all, I can merge them together with HKL2000 now, and I found it also can do "No merge original index" and merge different data sets with same unit cell by new version of HKL2000, which is better than old version -Original Messages- From:"Eleanor Dodson" Sent Time:2019-07-15

Re: [ccp4bb] challenges in structural biology

Hi James, 2 things come to mind. 1) What are the tools we can use for metals in structural biology? Note, I am biased here… 2) Micro electron diffraction methods - ability to use on small crystals (which speaks to Tom’s point) and a potential bridge between cryo-EM and X-ray diffraction

Re: [ccp4bb] Coot 0.9 curlew has no entry

Dear Paul, Thank you for your response and your time! In this case I will just try it again sometime later. Best, Chen On Mon, Jul 15, 2019 at 7:05 PM Paul Emsley wrote: > On 15/07/2019 12:37, Chen Zhao wrote: > > > > I am sorry to bother you, but I was trying to install the long range >

Re: [ccp4bb] challenges in structural biology

Hello Tim, I'm not sure this question is specific to crystallography- I believe the same can be asked of any experiment in any field? And if one wants to get into true costs- was it worth it to build the Large Hadron Collider to statistically prove that the Higgs boson exists? I'm guessing

Re: [ccp4bb] SA_flag vs PDB

Hmm….this is all a mess. If the objective is that the users can generate the EXACT map the depositor saw, I agree, the output of the Refmac mtz file with the map coefficients would be good. Alas, no can do, because the Fs are not the same as in the input file, if I am understanding

Re: [ccp4bb] Coot 0.9 curlew has no entry

On 15/07/2019 12:37, Chen Zhao wrote: I am sorry to bother you, but I was trying to install the long range refine, sphere refine, tandem refine, etc. utilities in coot 0.9 for cryo EM map. I was following the instructions on the youtube video, however, when I typed in curlew() in python

Re: [ccp4bb] SA_flag vs PDB

Hi Bernhard Oh dear, yes that's quite possible. But in any case we recommend _not_ to deposit the output from STARANISO: http://staraniso.globalphasing.org/deposition_about.html Cheers -- Ian Cheers -- Ian On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp wrote: > Hi Fellows – > > > >

Re: [ccp4bb] challenges in structural biology

If one were able to crystallise almost all proteins (and complexes) reliably and with good diffraction, that would make most people's lives much easier. So I would go with 1) as a grand challenge. Many of the rest follow on from not having 'good' crystals to start with. cheers, tom Tom Peat

[ccp4bb] SA_flag vs PDB

Hi Fellows - wondering if there is a particular reason the PDB cannot process a mtz file that in addition to FreeR_flag includes a SA_Flag column from StarAniso? Can there be no more than one I column type because that is automatically interpreted as the free flag?? Best, BR

Re: [ccp4bb] challenges in structural biology

Hi James,  7) or 8) What are a few different collection methods including at RT for serial crystallography data? Temperature vs global and site-specific radiation damage  --- RT serial crystallography             Temperature vs multiple conformers    Thanks, Minmin   > Dear James, > > 10) are

Re: [ccp4bb] challenges in structural biology

Hi James,  7) or 8) What are a few different collection methods including at RT for serial crystallography data? Temperature vs global and site-specific radiation damage  --- RT serial crystallography             Temperature vs multiple conformers    Thanks, Minmin   > Dear James, > > 10) are

Re: [ccp4bb] challenges in structural biology

Hi James,  7) or 8) What are a few different collection methods including at RT for serial crystallography data? Temperature vs global and site-specific radiation damage  --- RT serial crystallography             Temperature vs multiple conformers    Thanks, Minmin   > Dear James, > > 10) are

Re: [ccp4bb] challenges in structural biology

Hi James,  7) or 8) What are a few different collection methods including at RT for serial crystallography data? Temperature vs global and site-specific radiation damage  --- RT serial crystallography             Temperature vs multiple conformers    Thanks, Minmin   > Dear James, > > 10) are

Re: [ccp4bb] challenges in structural biology

Hi James,  7) or 8) What are a few different collection methods including at RT for serial crystallography data? Temperature vs global and site-specific radiation damage  --- RT serial crystallography             Temperature vs multiple conformers    Thanks, Minmin   > Dear James, > > 10) are

Re: [ccp4bb] challenges in structural biology

I know it is going to hijack the original topic but I could not help... “The reports of death of (macromolecular) crystallography are greatly exaggerated. If we believed the prognosticators, it has been dead since the 80s when some folks made the claim that the only relevant structures were those

Re: [ccp4bb] challenges in structural biology

I would wonder more if the biological questions you can *ask* with a (crystal) structure are sufficiently relevant to justify the resources. Sent from my iPhone > On 15 Jul 2019, at 22:08, Tim Grüne wrote: > > Dear James, > > 10) are the biological questions that you can answer with a

[ccp4bb] challenges in structural biology

Hello folks, I have the distinct honor of chairing the next Gordon Research Conference on Diffraction Methods in Structural Biology (July 26-31 2020).  This meeting will focus on the biggest challenges currently faced by structural biologists, and I mean actual real-world challenges.  As much

[ccp4bb] Coot 0.9 curlew has no entry

Dear all, I am sorry to bother you, but I was trying to install the long range refine, sphere refine, tandem refine, etc. utilities in coot 0.9 for cryo EM map. I was following the instructions on the youtube video, however, when I typed in curlew() in python scripting interface, I got a

Re: [ccp4bb] muti-crystal averaging

Do you mean these crystals have different unit cells? If so then DMMULTI is a useful technique.. Or do you mean you have collected isomorphous data from several crystals and want to merge that data? In that case BLEND will help you decide how isomorhous the data sets are.. Eleanor On Mon, 15

Re: [ccp4bb] coot crashing

On 11/07/2019 01:51, Tom Peat wrote: Just wondering if anyone else is having issues with Coot crashing (regularly, not just once in a while). Are you doing anything in particular before the crash? platform: /bin/uname core: #f No core file found. No debugging This is a message for

[ccp4bb] muti-crystal averaging

Dear all I want to average several sets of crystal data together, and I saw some paper used DMMULTI program in CCP4, but I didn't find this program in ccp4, but only find Blend in ccp4 which only used for unmerged reflection files. I wondering is there any programs could use HKL2000 processed

[ccp4bb] Postdoc in Pearl/Oliver lab at Genome Damage and Stability Centre, Sussex

Post-Doctoral Research Fellow : Structural Biology of DNA Single-strand Break Repair (Ref 1739) A Post-doctoral position funded by Cancer Research UK is available from 1st October 2019 in the laboratory of Prof. Laurence Pearl FRS and Dr. Antony Oliver in the Genome Damage and Stability

[ccp4bb] Head of Cryo-Electron Microscopy Core Facility

Dear structural biologists, Based on a successful application for large infrastructure, the Charité will establish a cryo-EM facility on its Campus in Berlin-Buch, with a particular focus on cryo-electron tomography applications. We seek a head for this facility at the earliest convenience.

[ccp4bb] Bidentate GLU vs two monodentate GLU in metalloproteins

Dear all, What is more preferable or conserved by evolution point of view between glutamate acting as bidentate ligand by its carboxylate group or two monodentate GLU at metal binding site in natural metalloprotein. I was thinking 2 GLU are better than one bidentate GLU because if one GLU gets

Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

Hello Kay, Yes, locks the whole machine means it is dead in the water- no mouse, no other windows can be activated, no sequence of buttons (e.g. Ctrl-Alt-Del, Ctrl-C, etc) to stop or bring anything back to life. What I would call a classic case of the machine crashing- the window with the

Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

Hi Tom, does "locks my whole machine" mean that you cannot open another terminal window? If you still can, use the "ps -ef | grep coot" command to find out if the coot process still exists, and note its process id ("pid"). If it does, remove it with "kill -9 ". Or does the window system