Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

Hi, If you're using Sharp for phasing, it'll refine the positions and occupancies of the heavy atoms that Shelx has picked up in the first stage. I used Sharp a long time ago but I'm pretty sure it still works that way. My 2p. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion Universit

Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

/sharp/wiki/index.cgi?RunAutoSharp You can also run autoSHARP via CCP4, if you link your installation to it. Best, Aaron From: CCP4 bulletin board on behalf of fuxingke Reply-To: fuxingke Date: Wednesday, October 11, 2023 at 12:02 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Ref

Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

Hmm - I can give you scripts to use SHELX? Eleanor On Wed, 11 Oct 2023 at 11:02, fuxingke wrote: > Dear Colleagues, > Reacently, for SAD experiment, I find SOLVE and SHARP can refine the > variables > of heavy atoms, such as occupancies, coordinates and thermal parameters. > But how to use

[ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

Dear Colleagues, Reacently, for SAD experiment, I find SOLVE and SHARP can refine the variables of heavy atoms, such as occupancies, coordinates and thermal parameters. But how to use SOLVE and SHARP to refine heavy atom in command line in linux? I don't find a script to do it. Who has

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Dear Elke, That seems to have done the trick. Can't thank you enough!!! I'm so happy. For future readers: ca6 alt loc A and residue 401 70% occ pa3 #1 alt loc B and residue 402 30% occ pa3 #2 alt loc C and residue 403 30% occ I could have probably done pa3 #1 and #2 as the same residue 402 as I

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

d7-dmarc-requ...@jiscmail.ac.uk> À: "CCP4BB" Envoyé: Jeudi 16 Février 2023 18:40:31 Objet: Re: [ccp4bb] Refinement of ligand with alternate chemical structure Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of the "Ligands" occupancy 0.5, mangled the B molecul

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC . It notes these atoms are too close but carries on refinement happily enough.. But when I read the structure into COOT and try to refine the A copy

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Stuart The sum of occ in these three is 1.3 and it looks like you put the occ in the B-factor column. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Dear everyone that replied, thanks so much for the help thus far. Just for info I’m using Coot for Windows version 0.9.6 EL and phenix.refine version 1.20rc4-4416-000 RE Eleanor: It appears my version of coot/refmac do not support separate ligands in the same space at <0.5 occupancy. As an ex

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Dear Stuart, you have to add   allow_duplicate_sequence_numbers() to $HOME/.coot.py in OSX or the appropriate place on Windows. For Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ directory for configuration - these can be found (added to) the directory in which Coot was

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

One may need to set a preference in Coot to allow such a situation to be viewed. Paul helped me but I can't find the email. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nw

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

I thought that REFMAC tolerated dual occupancies if the sum of the two conformers was <= 1.0? Eleanor Will test.. On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some > refine

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Hi Stuart, the answer, I think, is here: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Pavel On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic hexa-a

[ccp4bb] Refinement of ligand with alternate chemical structure

I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some refinement have noticed partial occupancy of it's hydrolysed form 2x A3, which has a cyclic 2'-3' phosphate on the terminal ribose. I tried fitting both ligands with 50% occupancy, but refinement doesn't allow them to occupy

Re: [ccp4bb] refinement of 0.73A data in shelxl

igand. It's there a way to use something similar like FVAR in a pdb > >> file? > >> > >> > >> > >> > >> Dr. Matthias Barone > >> > >> AG Kuehne, Rational Drug Design > >> > >> Leibniz-Forschungsinstitut

Re: [ccp4bb] refinement of 0.73A data in shelxl

stitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 From: bogba...@yahoo.co.uk Sent: Thursday, February 6, 2020 5:01:14 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refineme

Re: [ccp4bb] refinement of 0.73A data in shelxl

Sent: Thursday, February 6, 2020 5:01:14 PM > To: Barone, Matthias > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl > > > Hello, hope I can help. > > > OK, so here is the disp table... > > SFAC C H CL N O > > DISP $C

Re: [ccp4bb] refinement of 0.73A data in shelxl

(FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 From: bogba...@yahoo.co.uk Sent: Thursday, February 6, 2020 5:01:14 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl Hello, hope

Re: [ccp4bb] refinement of 0.73A data in shelxl

hone: +49 (0)30 94793-284 From: bogbasic@yahoo.co.uk Sent: Thursday, February 6, 2020 5:01:14 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl   Hello, hope I can help. OK, so here is the disp table... SFAC 

Re: [ccp4bb] refinement of 0.73A data in shelxl

le-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 From: bogba...@yahoo.co.uk Sent: Thursday, February 6, 2020 5:01:14 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl Hello, hope I can help

Re: [ccp4bb] refinement of 0.73A data in shelxl

Tuesday, February 4, 2020 9:24:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl   Dear Jon, in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like. The scattering factor is derived from the number next to the name. The name

Re: [ccp4bb] refinement of 0.73A data in shelxl

AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > -- > *From:* CCP4 bulletin board on behalf of Tim > Gruene

Re: [ccp4bb] refinement of 0.73A data in shelxl

esign > > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > > From:Pavel Afonine > Sent:Monday, February 3, 2020 7:14:25 PM > To:Barone, Matt

Re: [ccp4bb] refinement of 0.73A data in shelxl

> > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > > From:Pavel Afonine &

Re: [ccp4bb] refinement of 0.73A data in shelxl

14:25 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl   Hi Matthias, did you use correct model parameterization and optimal refinement strategy for the resolution? Such as: - Add H atoms; - Refine all but H atoms with anisot

Re: [ccp4bb] refinement of 0.73A data in shelxl

7:14:25 PM To: Barone, Matthias Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl Hi Matthias, did you use correct model parameterization and optimal refinement strategy for the resolution? Such as: - Add H atoms; - Refine all but H atoms with anisotropic ADPs

Re: [ccp4bb] refinement of 0.73A data in shelxl

Hi Matthias, did you use correct model parameterization and optimal refinement strategy for the resolution? Such as: - Add H atoms; - Refine all but H atoms with anisotropic ADPs; - Model alternative conformations (that one'd expect many at this resolution); - Add solvent (water, crystallization c

Re: [ccp4bb] refinement of 0.73A data in shelxl

Hello, sorry if this is a really obvious question, but have you used the ANIS option? I remember it is good at cleaning-up difference density around halogen atoms that sort of resolution.Jon CooperOn 3 Feb 2020 11:08, "Barone, Matthias" wrote: Dear ccp4 community Im having some problems solvin

Re: [ccp4bb] refinement of 0.73A data in shelxl

Maybe the figures were just contoured odd...but my recollection of a good 0.8 A map appearance is differentwhich might be consistent with the high Rf...a look at the high res data or images/stats might help? Best, br On Mon, Feb 3, 2020, 14:58 George Sheldrick wrote: > Dear Matthias, > > >

Re: [ccp4bb] refinement of 0.73A data in shelxl

Dear Matthias, That is very strange. First please repeat the shelxl refinement with the occupancy of the offending chlorine(s) in the .ins file changed from 11  (i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If that does not help I would be happy to look at it in confiden

Re: [ccp4bb] refinement of 0.73A data in shelxl

The maps look beautiful, but maybe the high resolution data is refining poorly. Not sure how to do this with phenix or SHELX but REFMAC gives you a plot of and v resolution. You sometimes see wild divergence in some resolution shells. Looking at Rfactors v resolution can also highlight such probl

Re: [ccp4bb] Refinement of Occupancy in Refmac

Hi Deniz, yes you can do that, though I don't know right now how B-factors are taken into account when refining occupancies. Anyway, in i2 you have to go to the advanced tab. There is a place to put keywords in (text area). There you put the right combination of keywords for your special cases. Re

[ccp4bb] Refinement of Occupancy in Refmac

Hello, when I add an alternative conformation of a residue in COOT, I have to set the occupancy of both conformers, but Refmac5 won't touch these numbers. Can I tell Refmac to check for the best fitting occupancies (in the Windows version of CCP4i2)? With kind regards, Deniz Üresin Institute for

Re: [ccp4bb] Refinement

Hi, Run your data through POINTLESS to check space group. Ray On Sun, 3/24/19, StrBio wrote: Subject: [ccp4bb] Refinement To: CCP4BB@JISCMAIL.AC.UK Date: Sunday, March 24, 2019, 12:17 AM ALL. I have data at 2.4 A in P21 sp gr, helical

Re: [ccp4bb] Refinement

In coot, select. Validate > Difference Map Peaks > Find Peaks Above 4 r.m.s.d > [Find Peaks] What do you see? Always remember, the real-space representation of your Rwork is the Fo-Fc map. The biggest peak or valley in this map is usually dominating your Rwork/Rfree. If you feel your Rwork/R

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

Betreff: [EXTERNAL] [ccp4bb] Refinement  

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote: >> >> Dear ???, >> >> Do you have any ice rings (even hardly visible ones) in your diffraction >> data? >> >> Best, >> >> Herman >> >> >> >> *Von:* CCP4 bull

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

ngs (even hardly visible ones) in your diffraction > data? > > Best, > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > ] *Im Auftrag von *StrBio > *Gesendet:* Sonntag, 24. März 2019 05:17 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betref

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

19 05:17 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] [ccp4bb] Refinement > > ALL. > > I have data at 2.4 A in P21 sp gr, helical protein. > Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics > oither Rfactor (by Phenix). Refmac quit same. > Sh

[ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

Dear ???, Do you have any ice rings (even hardly visible ones) in your diffraction data? Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio Gesendet: Sonntag, 24. März 2019 05:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Refinement ALL. I

Re: [ccp4bb] Refinement

In Refmac there is a plot of Rfactors v resolution, Could you high resolution data (or low for that matter) be particularly high? Eleanor On Sun, 24 Mar 2019 at 05:06, Lorenzo Briganti wrote: > If you’re sure about your refinement parameters and results, I would check > PDBredo just in case. I’d

Re: [ccp4bb] Refinement

If you’re sure about your refinement parameters and results, I would check PDBredo just in case. I’d go for better Rs, but maybe it’s not possible with your data. Best, Lorenzo domingo, 24 de março de 2019 01:17 -0300 de biophysics.w...@gmail.com : ALL. I have data at 2.4 A in P21 sp gr, he

[ccp4bb] Refinement

ALL. I have data at 2.4 A in P21 sp gr, helical protein. Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics oither Rfactor (by Phenix). Refmac quit same. Should I deposit it or look better data? Any suggestion? ##

Re: [ccp4bb] Refinement with native and anomalous data

>My advice is to simply cycle back-and-forth between the two data sets. Refine against your high-resolution data until that converges, then simply >switch to the other mtz file and use F+ F-, along with "anomalous wavelength" and probably "refine orefine no", unless you want to refine the >occupan

Re: [ccp4bb] Refinement with native and anomalous data

My advice is to simply cycle back-and-forth between the two data sets.  Refine against your high-resolution data until that converges, then simply switch to the other mtz file and use F+ F-, along with "anomalous wavelength" and probably "refine orefine no", unless you want to refine the occupa

Re: [ccp4bb] Refinement with native and anomalous data

Dear Piotrek You can find some info on the use of prior phase information in refinement with Refmac in Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. doi: 10.1107/S0907444911001314. Epub 2011 Mar 18. REFMAC5 for the refi

Re: [ccp4bb] Refinement with native and anomalous data

Dear Eleanor, I have used the ACORN previously for structure solution but I will have to read more about its functionality in structure refinement. I have run two Refmac jobs using either native or anomalous data with otherwise default parameters resulting in R/Rfree of 0.2013/0.2458 and 0.1862/0.

Re: [ccp4bb] Refinement with native and anomalous data

I think any decision depends on the resolution of your two data sets. If they are very different I would choose the higher resolution one. If that is the Anom data then I would use the anom signal at least in the first cycles to improve the phases.. Eleanor On Thu, 3 Jan 2019 at 14:59, Piotr Wil

[ccp4bb] Refinement with native and anomalous data

Dear CCP4 experts, I'd like to ask your opinion about using anomalous signal in refinement of crystal structures in addition to using high resolution native data. I am working on a series of structures for which I have collected two data sets (from the same crystal): 1 - native with higher resolut

Re: [ccp4bb] refinement papers

Hi Careina, On behalf of Pavel Afonine: This (and references inside) may be a start: http://scripts.iucr.org/cgi-bin/paper?S0907444912001308 Then may be you could reuse some of existing presentations from here https://www.phenix-online.org/presentations/ Best regards, Oleg Sobolev. On Mon, J

Re: [ccp4bb] refinement papers

Here are some nice papers: journals.iucr.org/d/issues/2012/04/00/ Best Misbha On Mon, 25 Jun 2018 at 14:26, Careina Edgooms < 02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello everyone > > I am giving talk about refinement and model building. I wonder if anyone > knows of latest r

[ccp4bb] refinement papers

Hello everyone I am giving talk about refinement and model building. I wonder if anyone knows of latest relevant papers on this topic that you could suggest for me?thank you Careina To unsubscribe from the CCP4BB list, clic

[ccp4bb] refinement / modeling of partly mobile domain

Any hints on what might work for modeliing a domain that seems to be there visible in part and parly not? (half ofan Ig-domain) - presumably the other end of the domain has larger ensemble of coordinate postions (attached from one end to other part of the same molecule and neighbors in the crys

[ccp4bb] refinement restraints for C-terminal amide

Hello, how does one specify C-terminal amidation of a peptide for REFMAC refinement? I intended to prepare link restraints between the C-terminal amino acid residue and a residue "NH2". But JLIGAND reports "Code 'NH2' does not exist in the library". On my system, $CLIB/data/monomers/n/NH2.cif exist

[ccp4bb] AW: [ccp4bb] Refinement at 4A resolution

von Appu kumar Gesendet: Mittwoch, 22. April 2015 23:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Refinement at 4A resolution Dear CCP4 Member, I seek your advice on the refinement issues at the low resolution 4A. I am trying to refine a membrane protein structure after getting the phases from MR

Re: [ccp4bb] Refinement at 4A resolution

Dear All, Sorry for the wrong pointless file. With this mail i have attached the pointless run file from the unmerged data. This file also suggests the C2221 spacegroup. Appu On 22 April 2015 at 17:40, Christian Roth wrote: > Hi Appu, > > you start already with a fixed spacegroup (scaled merged

Re: [ccp4bb] Refinement at 4A resolution

Hi Appu, you start already with a fixed spacegroup (scaled merged data) according to your pointless log. So you can't get another possible solution from pointless. Cheers Am 22.04.2015 um 22:28 schrieb Appu kumar: Dear CCP4 Member, I seek your advice on the refinement issues at the low res

Re: [ccp4bb] Refinement at 4A resolution

The Xtriage & Pointless logs don't show definitively that the space group is C2221 as they have been run on the merged data. You may need to check them with the unmerged data, and perhaps run molecular replacement in a lower symmetry such as C2 Phil On 22 Apr 2015, at 22:28, Appu kumar wrote:

[ccp4bb] Refinement at 4A resolution

Dear CCP4 Member, I seek your advice on the refinement issues at the low resolution 4A. I am trying to refine a membrane protein structure after getting the phases from MR using the PHASER. The soluble domain structure which comprises of 40% of protein has been used as template (sequence identity 8

Re: [ccp4bb] Refinement with phase/FOM and HL coefficients

Potentially there is more information in the 4 parameters HLA HLB HLC HLD which can describe a bi-modal distribution of phase probabilities( that would be generated by experimental phasing) than can be carried by the 2 parameter PHI FOM which will describe a uni-modal distribution. However if HLC=

[ccp4bb] Refinement with phase/FOM and HL coefficients

Dear all In a few places (Refmac and Phenix, maybe there are also others), there is an option to use either phase/FOM or HL for refinement and DM. Is there any difference between these two? The dataset in question is a Fe SAD dataset. Thanks. Mohamed

Re: [ccp4bb] Refinement with refmac05 and methionine density

ry University of Cambridge 80 Tennis >> Court Road Cambridge, CB2 1GA United Kingdom >> >> -------- >> >> >> *From:* jeorgemarley thomas >> *Sent:* Wednesday, November 12, 2014 8:16 AM *T

Re: [ccp4bb] Refinement with refmac05 and methionine density

; *Sent:* Wednesday, November 12, 2014 8:16 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Refinement with refmac05 and methionine density > > Dear All, > > I am refining the structure with refmac05, and after each refinement the > density around this methionine is flipp

Re: [ccp4bb] Refinement with refmac05 and methionine density

Kingdom From: jeorgemarley thomas Sent: Wednesday, November 12, 2014 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refinement with refmac05 and methionine density Dear All, I am refining the structure with

Re: [ccp4bb] Refinement of Iron-sulphur clusters

Dear Oliver, Since you mentioned my name let me try to confuse the issue. The iron atoms in Fe4S4 clusters can adopt different oxidation states, e.g. in HiPIPs and Ferrodoxins, and one might expect this to influence the geometry of the clusters. So maybe you would need several different sets of re

Re: [ccp4bb] Refinement of Iron-sulphur clusters

on 13/10/14 6:33 PM, Pedro Matias wrote: > In relation to this topic, I'd like to mention that SF4 has replaced FS4 > as the Fe4S4 monomer in the CCP4 monomer library. > > However, the dictionary values for bond lengths and angles are not > correct, and this is especially noticeable when the dict

Re: [ccp4bb] Refinement of Iron-sulphur clusters

gt; the cluster to the surrounding cysteines. >> >> HTH, >> Robbie >> >> Sent from my Windows Phone >> >> Van: >> Verzonden: 10-10-2014 18:07 >> Aan: CCP4BB@JISCMAIL.AC.UK >> Onderwerp: [ccp4bb] Refinement of Iron-sulp

Re: [ccp4bb] Refinement of Iron-sulphur clusters

stephen.c...@rc-harwell.ac.uk tel 01235 567717 From: "Oliver Smart" [osm...@smartsci.uk] Sent: 13 October 2014 12:09 To: ccp4bb Subject: Re: [ccp4bb] Refinement of Iron-sulphur clusters Stephen, Robbie advice is 100% correct. Be careful about

Re: [ccp4bb] Refinement of Iron-sulphur clusters

k > your cluster. You also need to make sure to provide LINK records to attach > the cluster to the surrounding cysteines. > > HTH, > Robbie > > Sent from my Windows Phone > > Van: > Verzonden: 10-10-2014 18:07 > Aan: CCP4BB@JISCMA

Re: [ccp4bb] Refinement of Iron-sulphur clusters

Sent from my Windows Phone Van: Verzonden: 10-10-2014 18:07 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Refinement of Iron-sulphur clusters Dear CCP4 BBers, I am currently refining a model of a protein containing three iron sulphur clusters using Refmac

[ccp4bb] Refinement of Iron-sulphur clusters

Dear CCP4 BBers, I am currently refining a model of a protein containing three iron sulphur clusters using Refmac (v5.8.0078) and am getting some unusual results. One of the clusters (3fe 4s) seems to behave resonably and the refined electron density looks very nice. The atoms in the others c

[ccp4bb] Refinement of 4 domain twin data

Dear All, Does anybody know if Phenix can refine the structure with 4 domain twin like refmac? If it can, how to write the input file? Best Xianchi

Re: [ccp4bb] Refinement problem

Rather hard to advise! Options are: a) The helical domain is wrongly positioned! b) There are scaling problems or swathes of missing data which can depress some parts of the electron density. If you use coot and reduce the contour level in this region, is anything sensible visible? A useful

[ccp4bb] Refinement problem

Hello All, I am new to low resolution refinement parametrization and regularization. Crystal diffracted with high anisotropy reaching to 3.5A in one direction and 4.5A other direction. I am refining a structure at 3.9A resolution. Protein has two domain connected trhough a linker and is packed as

[ccp4bb] Refinement

Hi all, I need to refine a structure keeping the ligands or some of the ligands intact (in same positions as before refinement). Please give me specific instructions if you are familiar with this procedure. I am using Refmac 5 in CCP4. Thanks so much for your help. Remie

Re: [ccp4bb] Refinement with new ligands to PDB

Thank you very much everyone for your comments. I will try your ideas and try to get this thing to work. I appreciate your help Meisam On Mon, Mar 31, 2014 at 7:21 PM, Meisam Nosrati wrote: > Dear CCP4ers > > I have crystallized a protein with a series of ligands that are not in the > PDB. >

Re: [ccp4bb] Refinement with new ligands to PDB

Dear Meisam, In the past I had similar problems, because of jligand and other cif generators can make errors when generate cif files, as it has been written before. I have solved these problems by using sketcher (ccp4) and PRODRG server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg). I u

[ccp4bb] AW: [ccp4bb] Refinement with new ligands to PDB

: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Refinement with new ligands to PDB Dear CCP4ers I have crystallized a protein with a series of ligands that are not in the PDB. I have made the pdb and the torsion libraries in the jligand and given them the new three letter codes, and then I try the

Re: [ccp4bb] Refinement with new ligands to PDB

On 01/04/14 00:21, Meisam Nosrati wrote: Dear CCP4ers I have crystallized a protein with a series of ligands that are not in the PDB. I have made the pdb and the torsion libraries in the jligand and given them the new three letter codes, and then I try the refinement in the PHENIX or CCP4, bu

Re: [ccp4bb] Refinement with new ligands to PDB

: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Meisam Nosrati Sent: Tuesday, 1 April 2014 12:22 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refinement with new ligands to PDB Dear CCP4ers I have crystallized a protein with a series of ligands that are not in the PDB. I have

[ccp4bb] Refinement with new ligands to PDB

Dear CCP4ers I have crystallized a protein with a series of ligands that are not in the PDB. I have made the pdb and the torsion libraries in the jligand and given them the new three letter codes, and then I try the refinement in the PHENIX or CCP4, but since these ligands are not in the librar

Re: [ccp4bb] Refinement of data with pseudo translation symmetry

Well - your R values will probably appear higher than normal - there will be zones where all reflections are weak.. but the maximum likelihood targets are meant to deal with this reasonably well. It seems to work and the maps usually look OK! Eleanor On 25 November 2013 22:31, Niu Tou wrote:

[ccp4bb] Refinement of data with pseudo translation symmetry

Dear All, Does any body know if the existence of pseudo translation symmetry will affect refinement ? If it does, is there any keyword or method to avoid it? Thanks! Best, Niu

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

As an update, this approach did not work in Refmac, but as Pavel suggested it worked fine with phenix.refine. --paul On 08/23/2013 11:51 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Paul, have you actually tried using the 'alternate location indicator' with two di

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

Hi Paul, I would have them both in PDB file with different non-blanc altLocs and arbitrary starting occupancies and that will work in refinement (in phenix.refine for sure, can't tell for other programs). Pavel On Fri, Aug 23, 2013 at 8:39 AM, Paul Paukstelis wrote: > Greetings, > > We have bee

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Paul, have you actually tried using the 'alternate location indicator' with two different residues? I would not be surprised if that would work with refmac. Best, Tim On 08/23/2013 05:39 PM, Paul Paukstelis wrote: > Greetings, > > We have been

[ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

Greetings, We have been working on a few DNA crystals in which the asymmetric unit contains a stoichiometric (or nearly so) mixture of two similar but distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but for a few of these there are some hints from the density for two diff

Re: [ccp4bb] Refinement of partly occupied water molecules

On Fri, Jul 12, 2013 at 1:08 AM, Stefan Krimmer < krim...@staff.uni-marburg.de> wrote: > in some of my macromolecular crystal structures with resolutions between > 1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are > detectable which show after assignment of a water molecule to t

Re: [ccp4bb] Refinement of partly occupied water molecules

You are desribing the reason many people limit their refinement to lower resolution! I think it is probably universally true that there are multiple conformations for sidechain/water networks at the surface, which we just dont model properly. If you are going to tackle the fine details you need to

[ccp4bb] Refinement of partly occupied water molecules

Dear all, I have a question concerning the refinement of partly occupied water molecules: in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecul

Re: [ccp4bb] Refinement against frames

9 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refinement against frames Dear Boaz, Indeed, small molecule crystallographers are routinely converting pixels into I's and can refine structures to very low R-values, but only to a limited resolution. The Bragg intensities are very strong, and b

Re: [ccp4bb] Refinement against frames

972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Loes Kroon-Batenburg [l.m.j.kroon-batenb...@uu.nl] Sent: Tuesday, June 25, 2013 1:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refinement against frames Dear Boaz, Indeed, small molecule crystallographer

Re: [ccp4bb] Refinement against frames

CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Monday, June 24, 2013 2:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refinement against frames -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear John, actually I am not a frien

Re: [ccp4bb] Refinement against frames

Dear Tim, With a full interpretation of the diffuse scattering as well how about papers becoming entitled:- The structure and dynamics of enzyme X As you intimate some diffuse scattering is crystal dependent ie phonons derived. Other aspects are however not correlated over multiple unit cells but

Re: [ccp4bb] Refinement against frames

Hi Tim, I don't follow your point...frames are just data, and with more information than after integration. The data after integration is also to some extent dependent on the beamline. It should indeed give a more accurate description of the crystal contents - whether that in turn will translate

Re: [ccp4bb] Refinement against frames

72-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Monday, June 24, 2013 2:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refinement against frames -BEGIN PGP SIGNED MESSAGE---

Re: [ccp4bb] Refinement against frames

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear John, actually I am not a friend of this idea. Processing software make an excellent job of removing the instrumental part from our data. If we start to integrate against frames, the next structural title might be something like "Crystal structur

Re: [ccp4bb] refinement hanging--what am I missing?

What is the relationship between the molecules in the spacegroups - it seems likely that in the bigger cell there is a NC translation of ~(1/2,y,z)? ? (A2 ~ twice a1) That can be checked by the native Patterson.. If so that gives a class of significantly weaker reflections for h odd, and that usu

Re: [ccp4bb] refinement hanging--what am I missing?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, just FYI: while this does not apply in the ccp4/mtz world, the fact you might be missing is that in some refinement environments merging is carried out by the refinement program so that the actual data can be kept unmerged and e.g. the informat

Re: [ccp4bb] refinement hanging--what am I missing?

c) and run molecular replacement for each option. It may also be that your problem lies elsewhere. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Monday, April 29, 2013 4:14 PM To: CCP4BB@JISCMAIL.AC.UK

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