Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

On 27/07/2022 01:44, Dale C wrote: Hi all, I recently updated my ccp4 package to Program suite v8.0.002 and i have now run into a few issues with other programs. The issues are highlighted below... - When i click 'Open in Coot' on any output through Phenix (so far only tested phenix.refine

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Ah yes, thank you. MacOS Moneterey v12.4. Dale. Dale Calleja PhD Student, Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade Parkville VIC 3052 Australia Email callej...@wehi.edu.au From: Joel Tyndall Date: Wednesday, 27 July 2022 at 11:19 am To:

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi Blaine, Thanks for your reply, I thought maybe this was related to my issue with ccp4, though I’ll also direct this to the PyMol mailing list as you suggested. I am currently using version 2.5.0, unfortunately neither type=pdb or type =cif seemed to fix the issue ☹ Dale. Dale Calleja PhD

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi Dale, Which version of PyMOL are you using? (PyMOL questions should really be directed to the PyMOL mailing list). Ancient versions of PyMOL may not accept cif files via fetch unless you include the type=cif​ keyword. To get the pdb file downloaded, try fetch 6wrh type=pdb​. I can download

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

PC, mac or linux? -Original Message- From: CCP4 bulletin board On Behalf Of Dale C Sent: Wednesday, 27 July 2022 12:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8 Hi all, I recently updated my ccp4 package to Program suite

[ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi all, I recently updated my ccp4 package to Program suite v8.0.002 and i have now run into a few issues with other programs. The issues are highlighted below... - When i click 'Open in Coot' on any output through Phenix (so far only tested phenix.refine and phenix.phaser), i no longer see

[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland -– final warning

Dear all This is a final reminder for this post. The closing date is the 27th of July. A postdoctoral position in the Integrated Structural Biology lab at The International Center for Translational Eye Research (ICTER) in Warsaw, Poland, is available for highly motivated biologists,

Re: [ccp4bb] symmetry possibilities

Thanks Eleanor. We tried to educate our crystals, through better purification and crystallization refinement, we got progress, but not enough to get totally well behaved ones. Yes, even at P212121, plot from pointless indicates, at least partial, twinning. Overlapping reflections, we did

Re: [ccp4bb] symmetry possibilities

Dear Ben, Hi Jorge,    I have had some similar cases. The twin fraction can vary during data collection on the synchrotron (different areas of the crystal can have different twin fractions).     Yes, Ben, this seems perfectly feasible to me. But your observation prompted me to think about

Re: [ccp4bb] symmetry possibilities

Dear Dom.     Yes, Zanuda must also give more insights, well pointed (it goes straight to my question "Should I look at anything else to establish twin P1 is the best way to refine this structure?"). By the way, though we have not gone through P1 in/extensively for while, a brief overview

Re: [ccp4bb] symmetry possibilities

Thank you, Edward, for sharing this. I will read through the (extensive) details of the work. J. On 7/22/22 10:25 PM, Edward A. Berry wrote: As for your second question, whether refining in a lower symmetry affects the R-factors, On 7/20/22 10:10 AM, Jorge Iulek wrote: Related, and a

Re: [ccp4bb] Comparing two datasets

Thank you all for your answers and suggestions. Pointless got the data I wanted. Mirek On Jul 26, 2022, at 9:09 AM, Clemens Vonrhein mailto:vonrh...@globalphasing.com>> wrote: CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to

[ccp4bb] Fwd: Postdoctoral Fellow position at University of Texas Health Science Center San Antonio

My research group at UT Health San Antonio is looking for a creative and self-motivated Postdoctoral Fellow to study the structures and mechanisms of nucleic acid enzymes. We will use X-ray crystallography, cryoEM, and enzyme biochemistry to address basic

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Comparing two datasets

Hi Mirek, I have absolutely loved this discussion of other options for comparing datasets! But to your original problem: To tell CCP4 where r is installed, you need to add this to your $PATH. You will want to figure out where r is installed on your computer and then add it to your .bashrc file

Re: [ccp4bb] Comparing two datasets

Dear all, [just to add some caveats in case future students see this thread and start cut-n-pasting commands to successfully create some kind of MTZ file of dubious content] Unless we're talking about some really old datasets (of historical interest) or a disastrous situation (all backups lost),

Re: [ccp4bb] Comparing two datasets

If you want to merge them then you can use Pointless/Aimless/ctruncate, with the warning that the conversion from F to I is not ideal, and ctruncate should be set to regenerate F from I just as sqrt ie not apply the truncate procedure again. Pointless supersedes combat for this conversion

Re: [ccp4bb] Comparing two datasets

Indeed Jon you are right. If you want to know whether to merge two dasta sets, use SCALEIT for analysis.. If You actually want to merge the data. best to go back to each unmerged and feed both into pointless/aimless etc, although you can cheat be letting pointless square the given Fs then merge

Re: [ccp4bb] Comparing two datasets

Hello again, as far as I can tell, the question is about two already merged/unique datasets which Mirek wishes to merge into one. As far as I can tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous differences, etc, and I don't know of a way that you could get it to

Re: [ccp4bb] Comparing two datasets

Dear Colleagues, Scaleit is a terrific program. Amongst its strengths already listed I would also mention its breakdown table with F so that in the strongest F reflections bin any systematic errors between the two data sets can show up if the Rfactor is greater than about 1%. Greetings, John

Re: [ccp4bb] Comparing two datasets

Not only does SCALEIT do the job - it presented useful plots and an informative log file.. Eleanor (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the columns from each Xtal will need different labels..) On Tue, 26 Jul 2022 at 09:45, Phil Evans wrote: > If you give

[ccp4bb] Improved EM validation with Q-score at the PDB

Dear Colleagues, Starting September 23, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will include the Q-score metric (Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations from the wwPDB/EMDB workshop on cryo-EM data management,

Re: [ccp4bb] Comparing two datasets

If you give Pointless Fs, it squares them to Is (not correct if the Fs have been derived from the truncate procedure, but not too bad). It will then give you a comparison. If you give the two datasets to Pointless, labelling them as different datasets, you can use Aimless to compare them But

Re: [ccp4bb] Comparing two datasets

I think that POINTLESS works with intensities rather than structure factors (I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed breakdown (R factors as a function of resolution and differences in terms of sigmas etc) than POINTLESS WILL. Cheers, Andrew > On 26 Jul

Re: [ccp4bb] Comparing two datasets

Hello Mirek, A very quick approach for that is offered by pointless: pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz or pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK You will obtain a table looking like that, taking into account to possible reindexing: Alternative indexing

Re: [ccp4bb] Comparing two datasets

Hi Mirek, I am pretty sure XSCALE will do that for you : https://xds.mr.mpg.de/html_doc/xscale_program.html If not, maybe have a look on SHELXC in SIR mode. Hope this help. Nicolas On 25/07/2022 21:52, Cygler, Miroslaw wrote: Hi, I would like to calculate the R-merge for Fs from two