Re: [ccp4bb] Reduces the RSRZ outliers in the wwPDB validation report

a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT

Re: [ccp4bb] access to the electron density maps of a PDB entry

Dear all, a bit of a background follow-up to this: On Tue, Jan 14, 2025 at 09:37:44AM -0500, Yong Tang wrote: > I do understand PDBe offers electron density maps (8hbk.ccp4 and > 8hbk_diff.ccp4 separately)- is that our go-to nowadays when we would like > to inspect the maps of any particular PDB

Re: [ccp4bb] replacing B-factor column and color accordingly

### > > 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 members of www.jiscmail.ac.uk/CCP4BB, a mailing > list ho

Re: [ccp4bb] Problem of data reprocessing with XDS

Dear Yimin, without wanting to preempt additional feedback that the XDS developers might be able to provide (concerning the changes within that July 2024 XDS version that seem to trigger the differences you see), may we suggest that you have a look at https://www.globalphasing.com/autoproc/wik

Re: [ccp4bb] Tools for identifying possible contaminants

SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *

Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

Dear Martin, On Thu, Jun 13, 2024 at 10:40:43AM +0100, Martin Malý wrote: > Thank you for the link. It would be great if https://proteindiffraction.org/ > (IRRMC) was rescued. They are back in business since a couple of months now - at least regarding new data appearing there. > I preferred this

Re: [ccp4bb] Rescale merged data?

Dear Randy, Harry et al, sorry for replying to several emails in one message - but as always, everything is connected ;-) On Thu, Apr 18, 2024 at 10:02:40AM +, Randy John Read wrote: > I’d like to add my strong agreement to what Robbie said, but also point > out a wrinkle. When the PDB runs v

Re: [ccp4bb] About Staraniso

g.org/ [23] https://www.globalphasing.com/autoproc/ReleaseNotes/ReleaseNotes-autoPROC_snapshot_20190301.txt [24] https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif [25] https://www.globalphasing.com/autoproc/wiki/index.cgi?RunningAutoProcAtSync

Re: [ccp4bb] About Staraniso

Dear Arpita, > Apologies if the below query seems very naive! Your query is not at all naive, it is very probing. Sorry for the necessarily long reply to your questions - but there are a number of topics you raise where we think a large amount of confusion still exists. Please note that this re

Re: [ccp4bb] Fwd: radiation damage and image discard

C.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *

Re: [ccp4bb] in memoriam of Raimond Ravelli

Very, very sad news. He had always so much enthusiasm, good nature and friendliness that it was pure joy to work with him on using radiation damage as a source of small differences to use for phasing. He will be sadly missed! Kind regards Clemens > Dear all, > > It is with profound sadness I

Re: [ccp4bb] Low resolution and high anisotropy

Dear Lande, On Wed, Oct 26, 2022 at 08:09:10AM +0100, Lande Fu wrote: > I noticed STARANISO processd the data all the way down to 1.7A, with > very poor stats on high resolution shell. Were you looking at the second table in the original email? It is not in a format I recognize as coming from STA

Re: [ccp4bb] Checking X-ray sequence (no more protein).

Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-

Re: [ccp4bb] Regarding the correct space group identification

cmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > > This message was issued to members of [ http://www.jiscmail.ac.uk/CCP4BB | > www.jiscmail.ac.uk/CCP4BB

Re: [ccp4bb] Comparing two datasets

>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> To unsubscribe from the CCP4BB list, click the following link: > >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] problems in Rfree-flags when refining with REFMAC and processing with STARANISO

Dear Vera, On Wed, Jul 13, 2022 at 10:13:28AM +0200, Vera Pfanzagl wrote: > You write that I should make sure REFMAC reads in the test-set from > the staraniso.mtz and does not replace it with a new one. This > would only be the case if it generates a new test set when I > initially import the re

Re: [ccp4bb] problems in Rfree-flags when refining with REFMAC and processing with STARANISO

orm, such a combination consists of just concatenating several mmCIF files together (as long as their data blocks have different identifiers). However, if additional decisions have been made between data processing and actual refinement (like enantiomorph, space groups, alternative indexing et

Re: [ccp4bb] problems in Rfree-flags when refining with REFMAC and processing with STARANISO

Dear all, On Mon, Jul 11, 2022 at 03:12:02PM +, Carrapa Nunes Dias, Joao Miguel wrote: > I had a similar case and I solved it using the PDB tool pdb_extract from: > https://pdb-extract.wwpdb.org/ > PDB Extract is a pre-deposition service for assembling structure files for > wwPDB OneDep depos

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

Dear Dom, On Fri, Jan 14, 2022 at 10:56:32PM +, Dom Bellini wrote: > Thanks for your inputs. I wonder why the PDB doesn’t allow to submit > two separate mtz files, Ideally, these would actually be mmCIF files since MTZ files (1) can not hold all meta data a PDBx/mmCIF compatible file could po

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

On Wed, Nov 03, 2021 at 12:54:00PM +, Ian Tickle wrote: > Suppose you had to compare two datasets differing only in their > high-resolution cut-offs. Now Rwork, Rfree and Rall will inevitably have > higher values at the high d* end, which means that if you apply a cut-off > at the high d* end

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

On Thu, Oct 28, 2021 at 06:28:05PM +0530, Shipra Bijpuria wrote: > I would first look at the dataset stats and define a resolution range > mainly based on I/sigI >1 and cc1/2 >0.5. Based on this, would take the > good resolution datasets only. Some probably obvious word of caution here: these (qui

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

ubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ######## > > To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Selfrotation problem for the experts

gt; -- > > [1] https://stetefeldlab.c > > [2] https://stetefeldlab.ca/ > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&

Re: [ccp4bb] Negative electron density

ce with harmonic > restraints, or otherwise tell your favorite refinement program to not move > them.  Your documentation may vary. -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT G

Re: [ccp4bb] Problem with peakmax

SIX sh environment: maybe more limited to other shells, but standardized and therefore much more portable since every UNIX-like system so far will always have /bin/sh available. Cheers Clemens *---

Re: [ccp4bb] Question about tncs and SAD phasing

following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are availabl

Re: [ccp4bb] Anomalous signal to noise details

Dear David, On Fri, Dec 18, 2020 at 11:53:08AM +, David Waterman wrote: > The paper "Substructure solution with SHELXD > " > (Schneider & Sheldrick, 2002) describes how > > data can be truncated at the resolution at which [ΔF to

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, coming back to those map questions again: On Wed, Nov 25, 2020 at 12:56:16PM +, Mooers, Blaine H.M. (HSC) wrote: > The question is about a Fo-Fc map and the replies have been focused on such > maps. > However, I question why you are bothering with Fo-Fc maps. > The ligand was soake

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/pol

Re: [ccp4bb] Quote source inquiry

Hi Robbie, On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote: > At the same time if you have a a more relaxed approach to restraints > than you might find systematic deviations in bond lengths. A test > for that has been in WHAT_CHECK for decades and it actually works > surprisingly w

Re: [ccp4bb] Completeness question

Dear Robbie, On Sat, May 30, 2020 at 08:36:06AM +, Robbie Joosten wrote: > I've been looking at some recent PDB entries that have much lower > spherical) completeness than reported in the coordinate file. One > reason for this is that the data were anisotropicly truncated, > another reason is

Re: [ccp4bb] Completeness question

>  DONE. > > > Best > Vincent > ps: again, the credit of this script goes to the globalphasing team who > kindly helped when I asked them for help with it. > > > > Le 01/06/2020 à 11:47, Clemens Vonrhein a écrit : > > Dear all, > > > > On Sat,

Re: [ccp4bb] Completeness question

> > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP

Re: [ccp4bb] neg density/high B on sidechains

; > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-- *

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear all, as a follow-up to our initial message (and similar to other activities from the MX community), we added some content to our BUSTER wiki at https://www.globalphasing.com/buster/wiki/index.cgi?Covid19 to show interested users how to (re-)refine existing PDB entries with BUSTER and how

Re: [ccp4bb] CCP4BB vs COVID19

tay healthy. Ditto! Cheers Clemens -- *------ * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear Julien, On Thu, Mar 19, 2020 at 08:47:20AM +, Julien Cappèle wrote: > Though I agree with you Clemens that raw images are amazing to work > with as you can use any software you are confortable with, we cannot > forget that depositing several TB of data for each lab would be bad > for ecol

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear Petr, On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote: > For those of you who are in touch with these data, would deposition > of unmerged intensities in P1 in the whole detector range instead of > complete dataset be good enough to „correctly“ re-evaluete the > structure? Or is

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Hi Andreas, On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote: > - The link to the raw data can be found inside the mmCIF file under > _pdbx_related_exp_data_set.data_reference. Whether it's also shown on one > of the PDB sites is up to the designers of these sides. I cannot find a

Re: [ccp4bb] problem in structure solution of multidomain protein

; need help or suggestion for this issue. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *------ * Clemens Von

Re: [ccp4bb] 8/ 2263 spots indexed XDS

gt; > -- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > Dr. Raphael Gasper-Schönenbrücher > > Crystallography and Biophysics

Re: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters

wrote: > seen in a high resolution map? > > There is at least one other similar feature??? > > Eleanor -- *------ * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Pa

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

Dear Ivan, On Mon, Aug 05, 2019 at 05:44:56PM -0400, Ivan Shabalin wrote: > Dear Kay, > > Thanks a lot for your answers! > > To my best understanding, REFMAC does not have an option of for restoring > reflections only in certain resolution shells. Remember that you can always do some simple (bu

Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

Clemens -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalpha

Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

ndiffraction.org, sbgrid,org or zenodo.org et al) :-) -- *------ * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK

Re: [ccp4bb] Combining MR and SIR phases

Dear Luke, sorry for the late reply, but e.g. autoSHARP would do the MR-XYZ combination (it doesn't really matter what XYZ is: SAD, SIRAS, SIR, MIR, MIRAS, MAD). See [1] for combining the two approaches. Cheers Clemens [1] https://www.globalphasing.com/sharp/wiki/index.cgi?RunAutoSharp http

Re: [ccp4bb] High Rfree in last Shell

lution, which already is rather low? > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *--

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

ny > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no.

Re: [ccp4bb] change in unit cell volume

k: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Cas

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

Dear Herman, On Thu, Feb 07, 2019 at 10:26:09AM +, Herman Schreuder wrote: > I did understand your question correctly and (at least for ligands) > the procedure I and also Diana Tomchick described, worked. However, > I just did a test with both Refmac and Buster and it seems that > these progr

Re: [ccp4bb] AUTOPROC error s

# > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-- * Clemens Von

Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

Marika, and Tove Sjogren. "Structural basis for ligand promiscuity in cytochrome P450 3A4." Proceedings of the National Academy of Sciences 103.37 (2006): 13682-13687. -- *------ * Clemens Vonrhein, Ph.D. vonrhein AT Gl

Re: [ccp4bb] Generating Additional Phasing Statistics

--- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > > > To unsubscribe from the CCP4BB list, click the followi

Re: [ccp4bb] old data

Ooops - typo: https://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings (thanks Harry). On Fri, Feb 01, 2019 at 11:31:14AM +, Clemens Vonrhein wrote: > Some resources with a wide range of information regarding specific > detectors (even going back to 2005-2010) mi

Re: [ccp4bb] old data

f you have received this transmission in error, please notify us immediately. > Thank you for your cooperation. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&

Re: [ccp4bb] VERY old mtz file..

link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House,

Re: [ccp4bb] ice rings

*** > > Charles Chen > > Research Instructor > > University of Pittsburgh School of Medicine > > Department of Anesthesiology > > ****** > > #

Re: [ccp4bb] processing hd5 files from Dectris detector

Dear Laurent, On Thu, May 31, 2018 at 02:58:52PM +0200, maveyrau wrote: > we recently collected many datasets on dectris detectors producing > hd5 files. I would like to use some auto processing tools to process > them (xdsapp, xdsme…). As far as I can say, xdsapp or xdsme cannot > process hd5 nat

Re: [ccp4bb] Problems with HEC in CCP4

of Enzyme Engineering > > > A.N. Bach Institute of Biochemistry > > > Russian Academy of Sciences > > > Leninsky pr. 33, 119071 Moscow, Russia > > > e-mail: e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com> > > > <mailto:e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com>> > > > > -- > Eugene Osipov > Junior Research Scientist > Laboratory of Enzyme Engineering > A.N. Bach Institute of Biochemistry > Russian Academy of Sciences > Leninsky pr. 33, 119071 Moscow, Russia > e-mail: e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com> -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *--

Re: [ccp4bb] Issues with latest XDS (20171218)

=== > > > > > > > > > > > >---- > >Forschungszentrum Juelich GmbH > >52425 Juelich > >Sitz der Gesellschaft: Juelich > >Eingetragen im Handelsregister des Amtsgerichts Dueren N

Re: [ccp4bb] Total occupancy of two conformations of one nucleotide is over 1.0? Need help!

no small molecule > here. > > > Any suggestions for occupancy refinement? I will appreciate your great help. > > > Best, > > Wei > > > > [cid:2b30f1a8-2a3a-4483-ac12-310f4bbed70b] > > > > > > -- *

Re: [ccp4bb] Problem with Mg2+ binding site refinement

> >> After refinement, in Mg2+ binding site negative density (red) has been > >> found as in pictures. I am using Phenix refine, and during refinement, > >> metal restrains were used. Herewith I have attached the refinement > >> statistics. > >> > &g

Re: [ccp4bb] Optimising data processing of a I432 dataset with 75% solvent content.

1462 120 343 > Mean((I)/sd(I)) 25.8 132.0 1.0 > Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.771 > Completeness99.8 97.6 100.0 > Multiplicity

Re: [ccp4bb] NCS difference

Dear all, On Mon, Apr 24, 2017 at 08:15:57AM +, Bert Van-Den-Berg wrote: > Not quite sure what you mean but I suppose you refined with NCS > restraints and the red bar means that your chains in those regions > are not identical. I would turn NCS restraints off during > refinement, with your re

Re: [ccp4bb] excluding residues from NCS

Dear Alice, in case you are still working on setting up NCS-restraints in refinement (especially excluding those residues from NCS-restraints that are truly different): BUSTER [1] can do this automatically through the use of so-called "pruning" of the local structure similarity restraints [2]. It

Re: [ccp4bb] solvent masks

k somewhere and include in map > calculation? > > Thanks for suggestions, > tommi -- *-- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *--

Re: [ccp4bb] sfall bug?

Hi Jens, I do get the same results when running sfall xyzin a.pdb hklout a.mtz mapout a.map

Re: [ccp4bb] Optimal settings for finding NCS from density

Dear William, since it is a question to CCP4bb, I might suggest a CCP4-based solution ... On Fri, Jul 03, 2015 at 04:24:04PM +, William Chao wrote: > What would be the best settings to look for NCS using > phenix.find_ncs_from_density on an elongated (~150A) molecule? No > coordinate is avail

Re: [ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

I think. Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *--

Re: [ccp4bb] XDS INP

coordinate system to be used: this often has to be identical for everything and all beamlines at a given synchrotron. Reaching perfection in an imperfect world ;-) Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT

Re: [ccp4bb] XDS INP

k. I'll look at your data, > > treating them confidentially of course, and tell you what I find. > > > > best, > > Kay > > > > > > > > > > > > > > >Dear Kay, > > > > > >I've tune th

Re: [ccp4bb] Sharp: Solomon density modification step

ing and improving those initial phases. Cheers Clemens > > On 28/01/2015 07:42, Clemens Vonrhein wrote: > >Dear Nicolas, > > > >On Mon, Jan 26, 2015 at 03:21:00PM +, Nicolas Soler wrote: > >>A quick question regarding the density modification interface via > &g

Re: [ccp4bb] Sharp: Solomon density modification step

Dear Nicolas, On Mon, Jan 26, 2015 at 03:21:00PM +, Nicolas Soler wrote: > A quick question regarding the density modification interface via > the Sharp interface. Which resolution range / radius of the solvent > sphere/ ncycles should be used for optimal result? I usually don't play around a

Re: [ccp4bb] R/R free reported values

why the difference. The structure is 1.0A resolution 2CWS. > > > Thank you, > > > FREE ONLINE PHOTOSHARING - Share your photos online with your friends and > family! > Visit http://www.inbox.com/photosharing to fi

Re: [ccp4bb] experimental phasing + MR

diocre results. > > I apologize for the long question, and I would greatly appreciate any > suggestions for how to combine all of these data into a workable map so I can > build out the rest of the structure. > > Thanks, > Gabriel -- ***

Re: [ccp4bb] autosharp error message

e. Hope that helps Clemens PS: you might want to ask on the sharp-discuss mailing list or have a browse the SHARP/autoSHARP wiki for tutorials etc ... more info at www.globalphasing.com/sharp/. -- ******* * Clemens Vonrhein, Ph.D.

Re: [ccp4bb] the f' and f'' of heavy cluster

ensity modification, averaging, model building etc. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***

Re: [ccp4bb] post to ccp4bb

as I understand this ... Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *---

Re: [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

roc/ http://www.globalphasing.com/autoproc/ReleaseNotes/ReleaseNotes_autoproc-1.0.2.html Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle P

Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?

; > >>>> Pointless is 99.6% sure it's orthorhombic and puts out an mtz file > >>>> in P212121 containing > >>>> I SIGI BATCH M/ISYM > >>>> > >>>> where the batch numbers are all 1 and ISYM runs from 1 to 8. > >>>> So f

Re: [ccp4bb] Process multiple data sets

... Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER

Re: [ccp4bb] help regarding structure solution

n tag? That's around 45-50kDa if I > > remember right. > > > > If not, I've had a decent amount of luck using in situ proteolysis to get > > crystals of degraded fragments. Try a limited proteolysis first overnight > > at 4C at varying concentra

Re: [ccp4bb] P321 space group reindex problem

y Crystallography, 2nd ed. Berlin: Springer-Verlag.]). For instance, for 2.5 Å data, a 0.6 Å change in the unit cell might be acceptable, whereas at 3.5 Å this could rise to 0.8 Å. Cheers Clemens -- *** * Clemens Vonrhein,

Re: [ccp4bb] problem in scaling the Zn-MAD data

ost modern data-processing and scaling programs will take care of that automatically anyway? Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * S

Re: [ccp4bb] Structure Determination combining X-ray Data and NMR

r, Saskia Villinger, Clemens Vonrhein, Christian Griesinger, Markus Zweckstetter, Kornelius Zeth(2008): Structure of the human voltage dependent anion channel. Proc. Nat. Acad. Sci. USA 105: 15370-15375. or http://www.pnas.org/content/105/40/15370.full It contains a fair amount of backgr

Re: [ccp4bb] ncs axis translation

ption doenst seem to be endoed anywhere (why??) ...stupid me... > > Thanks, > tommi -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park

Re: [ccp4bb] Merging with CAD files

Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***

Re: [ccp4bb] Archiving Images for PDB Depositions

listed in the supplemental). Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *

Re: [ccp4bb] Archiving Images for PDB Depositions

posited. > > > >There we go. > > > >Now the matter of actually getting these here is slightly harder but > >if anyone has an example I will work something out. Please get in > >touch off-list... I will respond to the BB in a week or so to feed > >back on how responses to this go :o) > > > >Best wishes, > > > >Graeme -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***

Re: [ccp4bb] Archiving Images for PDB Depositions

imilar to that we had with initial PDB submission (optional for publication) and then structure factor deposition. Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sherato

Re: [ccp4bb] To archive or not to archive, that's the question!

k for the user in return for maybe/hopefully saving a whole project 5 years down the line? Not a bad investment it seems to me ... Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global

Re: [ccp4bb] Linux vs MacOS for crystallographic software

Hi Sebastiano, On Thu, Sep 29, 2011 at 09:52:44AM +0200, Sebastiano Pasqualato wrote: > >> does this mean that SHARP works on a Mac? yes (since 2004), same for BUSTER (since 2009) and autoPROC. Cheers Clemens -- ***

Re: [ccp4bb] Help with deleting reflections from an mtz file

stuck.. > > Eleanor -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (ht

Re: [ccp4bb] Trouble compiling ccp4 in osx: stalled at "checking for working non-fixed mmap"

'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr > http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia > > -- > This message has b

Re: [ccp4bb] Newbie Installation Question

H"; then Otherwise you end up with LD_LIBRARY_PATH settings that could contain a dangling "...:" - not sure if that could mess up your environment? Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPh

Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0

rect permissions can only be set during packaging unfortunately. Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park

Re: [ccp4bb] Ghostview in CCP4 configure interface

t; > Greetings, > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3, Campus Cantoblanco > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/content/research/macromolecular/mvr

Re: [ccp4bb] Ghostview in CCP4 configure interface

with ghostscript (or any > other PS viewer). Or you can view them directly with the 'xplot84driver' program which comes as part of CCP4? Cheers Clemens -- ******* * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT

Re: [ccp4bb] [RANT] Publication Data Formats

table over three pages and get a reasonably good looking ASCII representation of it. Takes about 10 seconds ... Acrobat reader is not very good for selecting text in PDF files. I don't know about others, but xpdf is really good at it. Cheers Clemens -- *****

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