Re: [ccp4bb] Measuring angles between domains

2021-11-13 Thread Eleanor Dodson
Well I do this by overlapping one domain of protein A onto protein B - you can do that in coot - then overlap the second domain of the shifted A onto the second domain of B. The coot log file tells you omega phi kappa applied and kappa is your angle of interest... is that clear enough - I could

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

2021-10-28 Thread Eleanor Dodson
THis is always a difficult decision. More commonly I have worried about the best resolution cut off. Judge on high Rmerges? Keep the overall R value acceptably low?? etc etc.. I always come back to the map - is it sharper with the extra data? Is more unmodelled solvent showing up? etc.. But

Re: [ccp4bb] A strange problem related to MR

2021-09-08 Thread Eleanor Dodson
Sorry lande fu- solutions P4 also can also be on different origins. That is a polar spacegroup and any value along the c axis is acceptable. But probably the mr search for both models just sets that to zero... the r factors for two models being are so different is not so surprising. How well do

Re: [ccp4bb] A strange problem related to MR

2021-09-06 Thread Eleanor Dodson
You know there are alternative origins for P43212 - and a different MR search very often will opt for a different origin.. from CCP4 doc P4(123)2(1)2 - I4(1)22 N*origin* Xo Yo Zo 1 0. 0. 0. 2 0. 0. 0.5000 3 0.5000 0.5000 0. 4 0.5000 0.5000 0.5000 Use

Re: [ccp4bb] Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-31 Thread Eleanor Dodson
chains and 1 chain on a special position? I would vote for the latter. > > > > Best, > > > > Herman > > > > *Von:* CCP4 bulletin board *Im Auftrag von > > *Peer Mittl > > *Gesendet:* Freitag, 27. August 2021 10:17 > > *An:* CCP4BB@JISCM

Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

2021-08-31 Thread Eleanor Dodson
ATTACHED SOME CORRESPONDENCE WITH David Lawson re these issues/. Eleanor On Tue, 31 Aug 2021 at 10:29, Robbie Joosten wrote: > Hi everyone, > > Thank you for the replies so far on and off list, they are really helpful. > Feel free to keep them coming. > > Cheers, > Robbie > > > -Original

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-31 Thread Eleanor Dodson
cludes both the possibility of merohedral and pseudomerohedral twinning. >> In the latter case, the obliquity parameter can be set using the keyword >> OBL." >> >> I wonder since which CCP4 version (or date) this is the default behaviour. >> >> best wishes, &

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-30 Thread Eleanor Dodson
Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs in the highest possible symmetry for the crystal class - eh P6/mmm for a trigonal crystal, and expand the set to fill the actual space group. This means the Free R assignment is suitable if later the crystal symmetry is

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-27 Thread Eleanor Dodson
> refinement in P3221 would come up with the same occupancies for the > > alternative conformations for the "extra" chain on the 2-fold axis. It > > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a > > sublattice with P3221 symmetry and it'

Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-26 Thread Eleanor Dodson
Motto =mitti in predictive text! On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson wrote: > Great, motto. I think you have nailed it! Did you use tefmac for twinned > refinement? And if so what did it suggest the twin fraction is? > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl wro

Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-26 Thread Eleanor Dodson
Great, motto. I think you have nailed it! Did you use tefmac for twinned refinement? And if so what did it suggest the twin fraction is? On Thu, 26 Aug 2021 at 16:30, Peer Mittl wrote: > Yes, the data indeed seems to be twinned and the tNCS has masked the > twinning statistics, which is why I

Re: [ccp4bb] AW: [ccp4bb] chain on 2-fold axis?

2021-08-26 Thread Eleanor Dodson
I must admit in cases like this, my first thought is - could the space group be wrong? or is it twinned - quite common in this space group.. the normal twinning tests are sometimes misleading when you have non-crystallographic translation. I would reprocess the data as P32, generate a model with

Re: [ccp4bb] using chooch

2021-07-20 Thread Eleanor Dodson
r for the anomalous signal > for X-ray scattering at http://skuld.bmsc.washington.edu/scatter/ When > you choose Br instead of Grr, you find > http://skuld.bmsc.washington.edu/scatter/data/Br.dat, or you read your > values from the interactive plot > http://skuld.bmsc.washington.edu/scatter/AS

[ccp4bb] using chooch

2021-07-20 Thread Eleanor Dodson
Grr - stuck at home - what is f' and f' for Br??? All nicely tabulated on my desktop but not here.. So use chooch.. but it grumbles about file name null How can I make it happy? Any help gratefully received Eleanor eleanor@wombat cysbfull % chooch -e Br -e 0.92

Re: [ccp4bb] AW: Strange indexing problem

2021-07-05 Thread Eleanor Dodson
Your self rotation strongly suggests a different spacegroup - I would look back at the integration and processing before puzzling over cell volumes! Eleanor On Mon, 5 Jul 2021 at 16:00, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Rob, > > > > Wat is the Matthews number, would

Re: [ccp4bb] Strange indexing problem

2021-07-05 Thread Eleanor Dodson
Why you have this problem I cannot guess, but your self-rotation clearly shows 2 2 2 symmetry. Try another data processing system? Eleanor On Mon, 5 Jul 2021 at 14:54, Robert S Phillips wrote: > I collected data last week on crystals of tyrosine phenol-lyase obtained > under new conditions.

Re: [ccp4bb] problems with running PARROT

2021-06-25 Thread Eleanor Dodson
000 > 0.311 0.345 0.000 0.000 0.025 0.016 0.000 0.000 > 0.345 0.380 0.000 0.000 0.021 0.014 0.000 0.000 > $$ > > > Gamma 0.24162 > > Log likelihood: 2.920853e+04 Log likelihood (free): 0.00e+00 > > $TABLE :Cycle 1 SigmaA statistics:

Re: [ccp4bb] problems with running PARROT

2021-06-25 Thread Eleanor Dodson
The extract from the log file looks OK - can you send the whole log.txt? Eleanor On Fri, 25 Jun 2021 at 12:09, Savvas Savvides wrote: > Dear colleagues, > > I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a > MacBookPro (OSX 10.15.7) and keep getting the following error report

[ccp4bb] Jenny Glusker's 90th birthday

2021-06-17 Thread Eleanor Dodson
I know not many will have met Jenny in person but maybe more have read Crystal Structure Analysis - a Primer by Glusker and Trueblood. It is an excellent book, and widely plagiarized! Please send a message if you would like to Eleanor Dodson -- *From:* Miriam Rossi

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem with peakmax

2021-06-11 Thread Eleanor Dodson
As you know Paul I would like COOT to output a list of peaks into a "coordinate " file.. You can do it laboriously by hand using Add atom at peak position but that gets tedious... Eleanor On Thu, 10 Jun 2021 at 22:14, Edward A. Berry wrote: > On 06/10/2021 11:19 AM, James Holton wrote: > > > >

Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Eleanor Dodson
peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" < wrote: > Paul was a little too terse, perhaps. > In script form > > peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx > keywords in here > EOF-pmx > > at least that's what works for me in Csh. Bash proselytizers will

Re: [ccp4bb] TWIN?

2021-06-08 Thread Eleanor Dodson
First spacegrouop - trigonal spacegroups can also be indexed as C2 so it isnt so surprising that a P6/mmm should masquerade as C2. I would look very carefull at the POINTLESS symmetry scores and see if some are more convincing than others. But how I hate RNA & DNA - molecular replacement

Re: [ccp4bb] How can I refine the occupancy with Refmac?

2021-06-07 Thread Eleanor Dodson
James - could you send me a few examples to add to the documentation? Lockdown means I cant easily access my own examples - all trapped on the lab desktop.. Eleanor On Mon, 7 Jun 2021 at 17:18, James Holton wrote: > I wrote a script for auto-generating occupancy refinement relationships > for

Re: [ccp4bb] How can I refine the occupancy with Refmac?

2021-06-07 Thread Eleanor Dodson
In GUI2 the Advanced box allows you to do that eg RESO 10 3 say if you wanted to restrict resolution.. Eleanor On Mon, 7 Jun 2021 at 11:35, Marina Gárdonyi < marina@pharmazie.uni-marburg.de> wrote: > Hi, > > I didn't know that I can also enter keywords without a file! That is a > good note,

Re: [ccp4bb] How can I refine the occupancy with Refmac?

2021-06-05 Thread Eleanor Dodson
here is an extract from the documentation. is it a help? i will try to find examples. eleanor This keyword defines number of cycles of refinement. Occupancy refinement (version 5.6.0037) from Tidied up occupancy group id chain ... residue atom alt or occupancy group id chain ...

Re: [ccp4bb] Self rotation function

2021-05-23 Thread Eleanor Dodson
esn't necessarily imply a 4-fold axis (i.e. > a closed group). It could simply be 2 (or even 3) subunits related by a 90 > deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to > multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak > heights wo

Re: [ccp4bb] Self rotation function

2021-05-22 Thread Eleanor Dodson
rotation system - they could be relating distant monomers.. Cheers Eleanor On Sat, 22 May 2021 at 17:50, Ian Tickle wrote: > > Hi Eleanor > > On Sat, 22 May 2021 at 14:55, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> And several stron

Re: [ccp4bb] Shortest distance between side chains

2021-05-19 Thread Eleanor Dodson
Yes - contacts or distang gives you a list of distances. PISA a list of h bonds and salt bridges - all with associated sym ops. But none produce a complete table - PISA output prob the best. Eleanor distang gives you this sort of information but i guess it is far too detailed? R 125 NA R

Re: [ccp4bb] MR problem in muti-domain structure

2021-05-11 Thread Eleanor Dodson
Where did you find the tutorial files?? Eleanor On Tue, 11 May 2021 at 10:24, Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello, just to double check, I assume that you input the correctly > oriented and positioned structure of each domain from successive runs as a >

Re: [ccp4bb] solving difficult protein structure

2021-04-23 Thread Eleanor Dodson
Finding a solution will be very difficult then. Eleanor On Fri, 23 Apr 2021 at 21:11, Swati Gupta wrote: > My data is moderate anisotropic also with a high Wilson b factor greater > than 200 > > On Sat, 24 Apr, 2021, 01:19 Eleanor Dodson, > wrote: > >> If you were luc

Re: [ccp4bb] solving difficult protein structure

2021-04-23 Thread Eleanor Dodson
If you were lucky the new crystal might have the same cell and spacegroup as your model, but otherwiseThis is a case for molecular replacement.? My course of action using CCP4I2 Process data carefully and look for any warnings. Align your new sequence with the model using clustalw Edit the model

Re: [ccp4bb] Omit maps in phenix and ccp4

2021-04-07 Thread Eleanor Dodson
hough. > > Cheers, > > Dirk. > On 07.04.21 11:46, Eleanor Dodson wrote: > > Well - I use COOT for this sort of task, and dont trust the automated > tools. > my procedure is > load COOT - probably after a refinement cycle > set occupancy of ligand(s) to 0.00 (

Re: [ccp4bb] Omit maps in phenix and ccp4

2021-04-07 Thread Eleanor Dodson
Well - I use COOT for this sort of task, and dont trust the automated tools. my procedure is load COOT - probably after a refinement cycle set occupancy of ligand(s) to 0.00 ( Measures - residue information - change occupancy) Look at the environment critically . eg if an ARG or other bulky side

Re: [ccp4bb] AW: [ccp4bb] High Rs

2021-04-01 Thread Eleanor Dodson
Agree with Herman except re using refined model as search model. This will almost always return the answer you started from.. Eleanor On Thu, 1 Apr 2021 at 13:49, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear Sam, > > > > The first thing that would come to my mind would be

Re: [ccp4bb] High Rs

2021-04-01 Thread Eleanor Dodson
Obviously something is wrong or missing but not enough info here to diagnose.. Check data processing very carefully. Look at plots of Rmerge v batch - did the crystal die at some point? At least in CCP4 you can restrict merging to a range of batches.. Wilson plot shapely? Spikes in the Second

Re: [ccp4bb] Why do large blobs show up in the pores of my crystal when I do refinement?

2021-04-01 Thread Eleanor Dodson
Blind almost always mean something is there. But your resolution is low. Scaling procedures st that resolution can cause misleading features to appear. Q1. How good is your Wilson plot? If you used the ccp4 data scaling etc it will have given you plots and comments. If you send s log file that

Re: [ccp4bb] refmac twin refinement vs resolution limit

2021-03-29 Thread Eleanor Dodson
Well - I am not sure whether this has anything to do with twin refinement but resolution limits are often a bit iffy. First the low resolution discrepancy. The Free R is generated to a lower and higher resolution than any observation. The FreeR set is meant to be complete for any possible index

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

2021-03-17 Thread Eleanor Dodson
a twin crystal is the one > that looks single under the microscope and only intensity statistics reveal > that the diffraction comes from more than one crystal. > > If a crystal looks multiple, i do not call it a twin. Am i being too > meticulous on this? > Thanks! > > On 16 Mar 20

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

2021-03-16 Thread Eleanor Dodson
You usually detect twinning most reliably from the intensity statistics - CCP4I2 and Xtriage report those.. Eleanor On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi < marina@pharmazie.uni-marburg.de> wrote: > Dear all, > > thanks to all who helped me solving the question. You sent me a lot of >

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

2021-03-12 Thread Eleanor Dodson
Any twinning is due to overlapping diffraction patterns from two or more different crystal fragments. This means that the "intensity" measured is in fact the sum of two or more different I(hkl) s eg in your case* I(hkl) obs* actually equals *I(h k l ) + sc (I -h -k l)* . The diffraction can look

Re: [ccp4bb] What might sit between these two citrates?

2021-02-26 Thread Eleanor Dodson
Look at Amon peak in map? On Fri, 26 Feb 2021 at 10:40, Gregor Hagelüken wrote: > To follow up: I forgot to mention that there is no Mg2+ in the condition. > We have PEG4K, Sodium citrate, Ammonium sulfate. > Cheers, > Gregor > > > - > PD Dr. Gregor Hagelueken > Institute of Structural

Re: [ccp4bb] NCS/Pseudo-symmetry

2021-02-25 Thread Eleanor Dodson
Well - you are a long way from a solution! All those rotation angles are close to each other.. What is the cell? How similar is the model to your structure? Have you looked at the self rotation function? Eleanor On Thu, 25 Feb 2021 at 20:54, Muhammad Bashir Khan wrote: > *Hello everyone;* > >

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

2021-02-22 Thread Eleanor Dodson
Well - that doesnt look too bad - it is hard to see in a screenshot but presumably the N & C in the ring are correctly placed? Why is there positive density over the Fe? Are there other similar features elsewhere in the map which can be assigned to noise? Eleanor On Mon, 22 Feb 2021 at 15:27,

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

2021-02-19 Thread Eleanor Dodson
I have been following this discussion with interest, without having any informed opinions to throw in.. (Except as the daughter of an Australian farmer I still see myxomatosis as a blessing - my father said in his youth to make a living he spent 10months of every year trying to control the rabbit

Re: [ccp4bb] Challenging Molecular Replacement

2021-02-16 Thread Eleanor Dodson
Well - your LLG etc looks good but those two solutions have symmetry equivalent rotation angles so must be related by a translation vector. SOLU 6DIM ENSE ense_1 EULER 269.0 80.4 177.3 FRAC 0.24 -0.22 -0.07 BFAC -1.51 #TFZ==6.5 SOLU 6DIM ENSE ense_1 EULER 89.0 80.4 177.3 FRAC

Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

2021-02-09 Thread Eleanor Dodson
ry, > > John Innes Centre, > > Norwich, > > NR4 7UH, UK. > > Tel: +44-(0)1603-450725 > > Web: https://www.jic.ac.uk/people/david-lawson > > Email: david.law...@jic.ac.uk > > > > *From:* Eleanor Dodson > *Sent:* 09 February 2021 13:15 > *To:* David

Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

2021-02-09 Thread Eleanor Dodson
I took this up with pdbe but what with lock down and all I am not too sure what the decision was ( or whether there was one) maybe you could start a chat to the pdbe lot Our code was d- 1292109592. It was a mess - tony Wilkinson was depositing the data from the labs, I had been doing refinement

Re: [ccp4bb] TNCS and oligomeric state

2021-02-03 Thread Eleanor Dodson
I would look VERY carefully at your data processing. CCP4I2 report is a good place to start. The self rotation with the ring around the edge is hard to reconcile with two molecules in the asymmetric unit. Are the images clean or streaky? Do you have a photo of the crystal? And by the way - you

Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

2021-01-26 Thread Eleanor Dodson
I fell into the same trap this week. Apparently if in the first screen you tick the box Crystal is twinned” the interface resets the input data to FMEAN (or IMEAN if you have asked to use intensitirs) and you don’t need to say TWIN . Semi logical I guess but easy to miss. Eleanor On Tue, 26 Jan

Re: [ccp4bb] Question about tncs and SAD phasing

2021-01-23 Thread Eleanor Dodson
Well - I would start with a self rotation analysis. That non-cryst twofold and three folds would suggest something with 3-2 symmetry. I vaguely remember an insulin structure with the hexamer 3-fold in similar orientation.. And this paterson peak "one major off origin peak at 0.5 0.5 0.173" might

Re: [ccp4bb] Open position - data management in biophysics

2021-01-21 Thread Eleanor Dodson
It is a long time since I had any practical concerns with this issue, but some funding bodies are more flexible than others. Welcome gives project grants then leaves it up to the recipient to hire and plan. And I guess the big research institutes like the crick and lmb have similar systems. It is

Re: [ccp4bb] increased Rfree after ligand fitting refinement

2021-01-20 Thread Eleanor Dodson
Well - there are several possible reasons for that . The least pleasing is that you have built the ligand in the wrong place, but leaving that aside. When you add something to your model the coordinates are rather approximate and the B factors are usually set to some quite arbitrary value, so it

Re: [ccp4bb] possible solution with Phaser

2021-01-06 Thread Eleanor Dodson
First - test other spacegroups - your solutions have lots of 60 degree angles - and the space group is hexagonal - there can be confusion between cryst symmetry and homo-dimer symmetries. If you go back to the data processing and read the pointless output carefully for point group clues- Qs to

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
screenshot > > best, matthias > > > > 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 > ---

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
That polygon is not very useful I dont think. The statistics need to be given separately for structures solved at given resolutions. Eleanor On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson wrote: > Well - you dont give the resolution of your data or the "wilson B" which >

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
Well - you dont give the resolution of your data or the "wilson B" which will be recorded in the data processing log. If the resolution is 3A or less a) it is hard to refine a B value, and b) it certainly should be high.. So more information is needed. Eleanor On Mon, 4 Jan 2021 at 14:39, Silvia

Re: [ccp4bb] AW: [ccp4bb] Problem in finding a MR solution

2020-12-11 Thread Eleanor Dodson
is time. > > > > Best, > > Herman > > > > > > *Von:* CCP4 bulletin board *Im Auftrag von *Eleanor > Dodson > *Gesendet:* Freitag, 11. Dezember 2020 15:37 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Problem in finding a MR solution > &g

Re: [ccp4bb] Problem in finding a MR solution

2020-12-11 Thread Eleanor Dodson
Well - C2 is a sub cell for P3 so that isnt surprising, but a cell difference of 202 to 212 means it isnt isomorphous.. But an Rw Rf/ of 26/31 isnt bad for such low resolution data? Eleanor On Fri, 11 Dec 2020 at 12:01, Suraj Kumar mandal wrote: > Dear Sir, > > Yes, we have checked handedness

Re: [ccp4bb] Problem in finding a MR solution

2020-12-11 Thread Eleanor Dodson
Do all data sets have similar cell dimensions. P3i can be indexed in a variety of ways, (h k l ) (k,h,-l) etc - refer to documentation on reindexing.. - All *P3i* and *R3*: (h,k,l) *not* equivalent to (-h,-k,l) *or* (k,h,-l) or (-k,-h,-l) so we need to check all 4 possibilities: So

Re: [ccp4bb] Refmac not handling microheterogeneity?

2020-12-02 Thread Eleanor Dodson
Only a hunch but this works: ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65 N ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C ATOM

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

2020-11-24 Thread Eleanor Dodson
Another idea - you dont mention resolution., but possibly the ligand is very wobbly, and appropriate B values would range widely. Some refinement defaults restrain the whole "residue" B factors quite tightly to a mean value. There are ways to relax Bfactor restraints but you will have to read the

Re: [ccp4bb] R free rising

2020-11-02 Thread Eleanor Dodson
Yes, as Dale says when the FreeR goes up after minor rebuilding you have usually somehow picked up a different FreeR set.. This is almost certainly what causes this to happen - you say *This results in R free slightly lower than R work.* Small changes in a well refined structure dont change r

Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Eleanor Dodson
It is always hard to know when to stop tweaking a model.. We know from high resolution studies that many sidechains at the solvent interface have multiple conformations, and that as a result the water networks should also have partial occupancies. But usually correcting these details does not

Re: [ccp4bb] Tyr pushed out during refinement

2020-10-19 Thread Eleanor Dodson
You dont say what resolution your data goes to - certainly REFMAC and I guess PHENIX have restraints to prevent van der waal clashes. If there is high resolution data then these restraints can be overridden to some extent. Maybe set the occupancy of the PRO C=O to 0.0 and see where the TYR

Re: [ccp4bb] [RESOLVED]partially restrained mode?

2020-10-18 Thread Eleanor Dodson
Years ago with the help of a visiting student we tried to rationalise the refmac documentation. Alas the student left, and my html skills are pretty rudimentary but maybe it would help.. Eleanor On Sun, 18 Oct 2020 at 19:10, Boaz Shaanan wrote: > Hi Bernhard, > > > Always trust Google. A most

Re: [ccp4bb] Element type N+1

2020-10-15 Thread Eleanor Dodson
Hmm - I have never seen anything like that - the monomer for ARG has no N+1 elements.. Garib? Rob? Eleanor On Thu, 15 Oct 2020 at 15:08, Sam Tang wrote: > Dear colleagues > > I am trying to refine a structure with Refmac and the work completes > without any warning. However I am a bit puzzled

Re: [ccp4bb] Quest for resolution-sensitive substructure determination cases

2020-10-12 Thread Eleanor Dodson
I will look for examples but in practice I try to include rather than exclude data. (In fact follow the shelxd/e protocol slavishly allowing its automatic selection of data cutoff) When choosing a resolution cut off I think it is important to appreciate that the best test for correctness is the

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Contouring Patterson map?

2020-10-10 Thread Eleanor Dodson
Sorry - go back to CCP4i Under maps Calculate patterson ( diff - anom - native - whatever. Click polt harker sections Oh dear That is meant to produce a postscript file but on my new Mac - it doesnt work.. On Sat, 10 Oct 2020 at 16:24, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu>

Re: [ccp4bb] Can anyone hear me?

2020-09-21 Thread Eleanor Dodson
Well - I dont think one gets one;s own messages? Eleanor On Mon, 21 Sep 2020 at 10:07, Harry Powell - CCP4BB < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Folks > > Okay, you can stop replying to me now on this topic - I’ve had several > replies from people on the BB telling me

Re: [ccp4bb] Best protocols to advance a low resolution twin

2020-09-14 Thread Eleanor Dodson
Rezaul: You say *But I only see the 2nd domain with exact same unit cell that I have solved for 2nd domain's with same space group. * I am afraid if that is so that you probably have only crystallised the 2nd domain. Does that domain refine all right? Eleanor On Mon, 14 Sep 2020 at 09:02,

Re: [ccp4bb] Refmac use - water addition

2020-09-12 Thread Eleanor Dodson
You don’t say quite how you are doing this. There is an option in the i2 pipeline to add waters using coot when the r factor falls below some assigned value. This is done using COOT. One can debate whether it is a useful option or whether the user would be better o open COOT and supervise the

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-09 Thread Eleanor Dodson
h users’ responsibility to design correct restraints (it is > not ideal, not because we do not trust users but because the knowledge is > not easily transferable from one refinement to another). > > > Regards > Garib > > > > > On 8 Sep 2020, at 20:51, Eleanor D

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-08 Thread Eleanor Dodson
tetrahedral). If that is the case then you need >> specific links or restraints. If my reading of your numbers is correct then >> there could be some chemistry change of the surrounding residues. >> >> If it is not structural Zn then it is likely that coordination is 6. But

Re: [ccp4bb] Best protocols to advance a low resolution twinned MR map

2020-09-08 Thread Eleanor Dodson
Hmmm - not much help, but MR can work with twinned data .. What's the sequence match between your models and your protein? And do you expect them to form a dimer? Presumably you found the d3:d3 dimer using MR? I would be a bit worried that the twinning could mislead a dimer search - are the two

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-08 Thread Eleanor Dodson
mbers correctly: none of your Zn > > atoms is structural (4 coordinated tetrahedral). If that is the case > then you > > need specific links or restraints. If my reading of your numbers is > correct > > then there could be some chemistry change of the surrounding residues.

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-08 Thread Eleanor Dodson
e in the dictionaries but the angles involve three > different residues so these cannot be in the current dictionary. We could > add the program that generates these restraints to CCP4 though. > > Cheers, > Robbie > > -Original Message- > From: Eleanor Dodson

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-08 Thread Eleanor Dodson
residues so these cannot be in the current dictionary. We could > add the program that generates these restraints to CCP4 though. > > Cheers, > Robbie > > > -Original Message- > > From: Eleanor Dodson > > Sent: Tuesday, September 8, 2020 11:38 > >

Re: [ccp4bb] metal coordination at low resolution - restraints

2020-09-08 Thread Eleanor Dodson
Robbie - could that be added to the distributed dictionaries? Zn binding is common and at low resolution distance restraints are not enough.. Eleanor On Tue, 8 Sep 2020 at 10:33, Robbie Joosten wrote: > Hi Anna, > > Yes you can do this in Refmac by adding external restraints. If you have >

Re: [ccp4bb] AW: Going back to Coot 0.8

2020-09-04 Thread Eleanor Dodson
Dear Users - yes , I had shared my frustrations with Paul, mostly caused I must say because COOT now worries (excessively I think) about atom clashes and wouldn't let me drag an ARG or HIS or GLU into the obvious density till I had deleted any rogue waters.. However there are real gains - Tandem

Re: [ccp4bb] Going back to Coot 0.8

2020-09-04 Thread Eleanor Dodson
Not the only one Paul!! On Fri, 4 Sep 2020 at 09:37, Schulz, Eike-Christian wrote: > > > > > > > > > > > > > > > > > Dear Paul, > > > > > > I have been working with coot for over 10 years now with little reason to > complain. > > > > > > > However, in spite of trying for a few months now, I am

Re: [ccp4bb] Stuck with Refinement

2020-08-06 Thread Eleanor Dodson
Dear Silvia, I look at those stats in the log file and worry about your data processing. There are some wild outliers in the measurements Unit cell: (129.59, 129.59, 118.84, 90, 90, 120) Space group: P 61 2 2 >From the log file: outliers Miller Index : Intensity : Sigma : Bin Mean Intensity

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-31 Thread Eleanor Dodson
Is the R factor for the best solution really > 40% - if so there must be some major errors to correct. Eleanor On Fri, 31 Jul 2020 at 11:08, John R Helliwell wrote: > Dear Rafal, > The difference map you show in your attachment has an echo of the main > structure sort of look. So, I suggest you

Re: [ccp4bb] real real-space-refinement

2020-07-29 Thread Eleanor Dodson
Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real real-space-refinement of a protein against a > cryo-EM map; not the mtz-based Refmac approach. A quick internet search > produced a

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-29 Thread Eleanor Dodson
Sometimes ghost like this mean there is a spacegroup error - absences can be the result of the non-crystallographic translation and not be truly indicitive of the spacegroup. what is the possible spacegroup and what is the NC translation vector? Eleanor On Wed, 29 Jul 2020 at 14:13, Schreuder,

Re: [ccp4bb] Question about P3, H3 and R3 space groups

2020-07-22 Thread Eleanor Dodson
> > > The original reference for the H cell is the very first edition of Int. > Tab.: > > Hermann, C. (1935). Internationale Tabellen zur Bestimmung von > Kristallstrukturen. Berlin: Gebrueder Borntraeger. > > Cheers > > -- Ian > > > On Wed, 22 Ju

Re: [ccp4bb] Question about P3, H3 and R3 space groups

2020-07-22 Thread Eleanor Dodson
* > > > On Wed, 22 Jul 2020 at 14:51, Nicholas Keep > wrote: > >> >> >> >> ---- Forwarded Message >> Subject: Re: [ccp4bb] Question about P3, H3 and R3 space groups >> Date: Wed, 22 Jul 2020 14:41:27 +0100 >> From: Elea

Re: [ccp4bb] Question about P3, H3 and R3 space groups

2020-07-22 Thread Eleanor Dodson
But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts (⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ?? Eleanor On Wed, 22 Jul 2020 at 14:32, Nicholas Keep wrote: > I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' >

Re: [ccp4bb] Question about P3, H3 and R3 space groups

2020-07-22 Thread Eleanor Dodson
This does seem confusing! Maybe the International tables have changed, but in my copy spacegroup 143 is labelled P3 Spacegroup 146 is equivalent to P3 with translations 1/3,2/3.2/3 and 2/3,1/3,1/3 is called rhombehedral This can be indexed with. "a=b=c in the rhombehedral setting" and labelled

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Eleanor Dodson
You can change the cell dimensions without spoiling the map fit too much, but obviously you need to convert deposited orthogonal coordinates back to fractional using the given SCALEi matrix, than re-orthogonalise with the modified cell.. Eleanor On Thu, 16 Jul 2020 at 13:01, Schreuder, Herman /DE

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Eleanor Dodson
EU member and > Sweden > not yet (so Uppsala couldn't be formally involved) :-) > > Did Victor look into this too? I remember Gert doing it. And maybe Tom > Oldfield? > > Best wishes, > > --Gerard > > > > On Thu, 16 Jul 2020, Eleanor Dodson wrote: > >

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Eleanor Dodson
Hmm - remember Gerard, the EU Validation initiative in the 1990s? We analysed these effects, or at least Victor Lamsin did, and we applauded him. Cheers Eleanor On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein wrote: > Hi Robbie, > > On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

Re: [ccp4bb] Quote source inquiry

2020-07-14 Thread Eleanor Dodson
True but who would claim it was On Tue, 14 Jul 2020 at 21:22, Bernhard Rupp wrote: > Hi Fellows, > > > > afaicrimps (as far as I can recall in my progressing senility) someone > once wrote/stated/cursed somewhere that “Macromolecular refinement is not a > small molecule structure determination

Re: [ccp4bb] Domain Motion Analysis

2020-07-08 Thread Eleanor Dodson
Well - I use standard software. Use GESANT or some such program to fit Structure 2 A to Structure ! A only - output wilh have all A B C but only A has been fitted// Now fit Structure 2 B from fitted structure to Structur 1 B . It will give you a PHI CHI Kappa needed to rotate B2 to B1 Is that

Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Eleanor Dodson
ow, users... Asking couple thousands people with combined > expertise of a few thousands of "X-ray crystallography" years, should > provide deeper insight into needs of community, than asking programmers > around. > > D. > > On 2020-07-07 12:17 PM, Eleanor Dodson wro

Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Eleanor Dodson
at. > Just my 2 cents. > > Cheers > Christian > > > On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh < > vaheh.oganes...@astrazeneca.com> wrote: > >> … and how all these changes being justified? >> >> >> >> *From:* CCP4 bulletin bo

Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Eleanor Dodson
on behalf of christianroth...@gmail.com> wrote: > > > > yes Eleanor is right. command line still works.[image: :-)] > > fft is also in 7.1 distribution. > > > > > > > > On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson > wrote: > > Oh Lau - how

Re: [ccp4bb] Accessing full list of programs in CCP4I2

2020-07-07 Thread Eleanor Dodson
Oh Lau - how I miss that list! But if you just run fft online it is still distributed..wombat:Downloads eleanor$ fft hklin mapout LABIN FP= and so on.. On Tue, 7 Jul 2020 at 14:22, Christian Roth wrote: > Hi Kelvin, > well fft as single program is kind of not longer supported as

Re: [ccp4bb] Twin law definition in REFMAC5

2020-07-06 Thread Eleanor Dodson
Is that twin law possible? Presumably the cell lengths for b and c are close but you are swapping a 2fold axis along c for a 21 axis along b? Eleanor On Tue, 7 Jul 2020 at 05:36, Petr Kolenko wrote: > Dear colleagues, > I have a crystal with space group P21212 and merohedral twinning according

Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-03 Thread Eleanor Dodson
You can create a link in COOT.. Eleanor On Thu, 2 Jul 2020 at 16:10, Cristina Machon wrote: > Dear all, > > I am writing regarding a problem we are facing with the refinement of a > structure. We would really appreciate it if anybody could suggest how to > set up geometrical restraints for a

Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

2020-06-21 Thread Eleanor Dodson
*Please* dont throw good 1.8A data for the sake of statistics! You should see more detail along certain directions You will publish your structure providing honest details of the anisotropy (I hope..) but it is the map quality that matters .. Eleanor On Sun, 21 Jun 2020 at 15:16, Matthew Snee <

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