Re: [ccp4bb] Rfree going up after refinement

I really need more information to comment properly. However just check that you are using the same reflections for both Rfree calculations. An Rfree of 26% seems low to me from a Se met phased structure at 2.1A - there are usually small corrections to be made, What is the Rwork? Maybe attach the

Re: [ccp4bb] According correct space group assignment...

Is this another example of crystallising the reagent and not the desired material? No wonder molecular replacement failed with a DNA search model . Eleanor On 25 April 2018 at 20:06, George Sheldrick wrote: > Dear Rafal et al, > > With some help from Kay I think that I could find out what is ha

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should* NOT *appear in a list devoted to GLU!! Well spotted.. Eleanor On 26 April 2018 at 10:34, Chris Richardson wrote: > Many thanks for explaining where it is going awry. > > Looking at GLU.cif in the monomer library that is part of the CCP4 > distribution, it

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

Well - if you use reindex to change the reflections from I213 to P1 the log file gives the rotation matrix need to convert I213 coordinates using the same convention. There are various clever inputs to reindex which allow you to do this Then you can use pdbset xyzin I213.pdb xyzout P1.pdb givin

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

= ( 1.0 -0.5 0.0 ) ( y) (z') ( 0.0 -1.00000 1.0 ) ( z) On 16 May 2018 at 22:20, Eleanor Dodson wrote: > Of course you need to give pdbset the new cell too... > E > > On 16 May 2018 at 22:20, Eleanor Dodson wrote: > >> Hmm - I think yo

Re: [ccp4bb] Predicting self-rotation function peaks from coordinates?

Hmm - PISA first to make the most likely assembly. of A B C D etc.. Then GESAMT to match A to B , A to C ,. ... B to C , etc That gives "self rotations" in polar (most useful) , Euler, and matrix.. That could all be scripted - Eugene? But of course self rotation lists do not necessarily give th

Re: [ccp4bb] Regarding symmetry notion in coot

Paul - where and what is the definition of this line?? eleanor On 21 June 2018 at 17:29, Paul Emsley wrote: > > On 20/06/18 20:49, Anurag Misra wrote: > > What is the meaning of the last field — the one in curly brackets -- that > describes the symmetry transformation of a given molecule in coo

Re: [ccp4bb] Regarding symmetry notion in coot

And so does MOLREP.. Phaser too please? E And Paul - yes; please cut and paste.. E On 21 June 2018 at 20:00, George Sheldrick wrote: > For small molecules, programs such as SHELXT move the structure to be as > near as possible to the center of the unit-cell, not the origin. Failure to > do so

Re: [ccp4bb] Unidentified electron density blob

Hmm - is the refinement complete? Maybe the GLU on the right could be moved to use some of that greenness? I try to make all sensible corrections, then check blobs.. Eleanor On 3 July 2018 at 04:22, zaigham mahmood khan wrote: > Uma, that is not something that we see regularly in the crystal > s

Re: [ccp4bb] disulfate bond ?

Hmm - the "S" atoms look too close - S=S bond ~ 2A Eleanor On 4 July 2018 at 07:26, 张士军 <21620150150...@stu.xmu.edu.cn> wrote: > Hi all > > I got a structure which has COA in it, and the SH in the tail of COA > is very close to the SH side chain of Cys in the structure. I don't know > whether it

Re: [ccp4bb] R-flag choose

FreeR flags are a bit of a pain - there is the number you should select, then how to compensate for non-crystallographic symmetry and putative twinning. Vilmos has written a useful Rfree assignment tool which covers possible twinning problems. It selects FreeR flags for the highest Laue symmetry c

[ccp4bb] salt bridges etc..

How do people decide on what is a salt bridge within a molecule and how to count them for those Tables? I have been looking at 2z2f - paper claims some score..- But there are several residues in alternate conformation with NZ A to OE1Aand NZ A to OE1B and NZ B to OE1B etc Is that one salt

Re: [ccp4bb] salt bridges etc..

in Xray if we > have good crystals. It does not matter, however, how many local > conformations we observe. It is just one salt bridge, and its energetic > contribution to protein folding remains (very roughly, and this is > practical experience for which no good theory exists) about 1kCal

Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an anomalous map, and looking at relativr peak heights for your known S positions and the putative sulphate or phosphate. There are small differences in the expected f" at most wavelengths. Chemical arguments are doubtless bet

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

How many molecules in the asymmetric unit? and is there a non-crystallographic translaton? Eleanor On 8 August 2018 at 15:29, Kajander, Tommi A wrote: > Hi, > Any clues why the followting happens: pointless (and just looking at the > XDS output) clearly tells there is one screw axis in P-ortorh

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

l quality in some > directions - overall data is not great... > > Best, > Tommi > > > Kohteesta: Eleanor Dodson > Lähetetty: keskiviikko 8. elokuuta klo 17.46 > Aihe: Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions > Vastaanottaja: Kajander, Tommi A &

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

Well that is pretty obviously P 2 21 2 - h 0 0 and l 0 0 are obviously present.. The 0 k 0 absences could be generated by a nc translation of x, 1/2, z - do you have that? Twinning is unusual in P2/mmm but possible of course - can you send the pointless log file? Eleanor On 9 August 2018 at

Re: [ccp4bb] Normalization of B-factors

I wouldnt have thought so. There is a B factor plot as part of CCP4I2 - does that show any pattern of differences between ligand and environ,ment? Eleanor On 9 August 2018 at 10:54, Santhosh Gatreddy wrote: > Hi all, > > I have to compare the B-factors of three of my ligand bound structures of

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

These problems are a pain! My (half-baked) thoughts 0) Yes - get rid of all junk images etc and inspect the frames - we have had a case where MR would not work for the "best" crystal as processed by XDS, but when we looked at the images there was clear streaking and other technical problems. t

Re: [ccp4bb] tCNS and space group determination

Can you attach the refinement log? Eleanor On 10 August 2018 at 16:57, Marcelo Liberato wrote: > Dear Randy, > > Thank you very much for answering. I followed your suggestions but, > unfortunately, I couldn't get a reasonable electron density map after MR > and refinement. > > > First I would l

Re: [ccp4bb] tCNS and space group determination

Actually Marcelo - Refinement to an R of 41% is pretty good for an MR solution! On 10 August 2018 at 18:42, Eleanor Dodson wrote: > Can you attach the refinement log? > > Eleanor > > On 10 August 2018 at 16:57, Marcelo Liberato > wrote: > >> Dear Randy, &g

Re: [ccp4bb] tCNS and space group determination

arch select the most likely spacegroup of the 8 possible. You cant even limit the b axis to be a screw axis . Your refinement behavior looks OK, but the maps will look bad with spurious reflections in the list.. Eleanor On 10 August 2018 at 19:02, Eleanor Dodson wrote: > Actually

Re: [ccp4bb] tCNS and space group determination

e log files from aimless, MR and refmac >> for P2 (in two different cells) and P222 data. >> I agree that MR seems very good (in all cases), but the final density >> maps are always bad. Maybe the data has problems that I am not dealing >> with. >> >> Kind

Re: [ccp4bb] tCNS and space group determination

rent cells) and P222 data. > > I agree that MR seems very good (in all cases), but the final density > maps are always bad. Maybe the data has problems that I am not dealing > with. > > > > Kind regards > > > > Marcelo > > > > Em sáb, 11 de ago de 2018

Re: [ccp4bb] Protein is dimmer in solution, hard to build two chains in crystal structure

75% solvent is not uncommon, and such crystals often only diffract to 3A. Eleanor On 20 August 2018 at 10:24, SUBSCRIBE CCP4BB Zhu Qiao wrote: > Hi All > > My protein is dimer both in protein buffer and crystallisation reservoir, > which is confirmed by calibration column Supderdex 200 10/300 in

Re: [ccp4bb] coiled-coil "degree"

In cases like this I use PISA for the first analysis - it will give buried surface area - h bonds, salt bridges etc, then work up from there. Eleanor On 28 August 2018 at 14:43, Anastassis Perrakis wrote: > Dear Jorge, > > The “coiled coil” has a formal definition - not all interacting helices >

Re: [ccp4bb] unexpected errors in LSQKAB

N1+ ANISOU 22 NH1 ARG A 415732 10019 13448 1911785 -419 N1+ On 10 September 2018 at 10:36, Eleanor Dodson wrote: > Charlie - I will try to check this, but cant read your pse file - can you > find another format? > > Thanks Eleanor > > On 8 Septe

Re: [ccp4bb] unexpected errors in LSQKAB

s do use the charges to modify the scattering > factors and write them out again. One hopes that this problem is solved > soon. > > Sorry for straying off topic. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf

Re: [ccp4bb] unexpected errors in LSQKAB

ou can see, even though the residues are, as far as > I can tell correctly indicated, the rotated file is off by about 90 degrees. > > Many thanks for any help. > > Charlie > > > > On Sep 10, 2018, at 5:36 AM, Eleanor Dodson > wrote: > > Charlie - I will try to c

Re: [ccp4bb] unexpected errors in LSQKAB

oli one is now rotated by ~ 90 degrees and fits quite well.. There is a lot of unmatched stuff of course for the Ecoli one but that shouldnt prevent the fit.. Eleanor On 10 September 2018 at 12:53, Eleanor Dodson wrote: > Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says >

Re: [ccp4bb] [i2dev] FW: CCP4i2 Refmac TWIN failing

*Q to ccp4i2dev..* Hello, I’m not sure whether this is a refmac issue or a ccp4i2 issue but we have recently solved the structure of a protein which appears to be twinned in the space P43 with 10 molecules in the asymmetric unit. When we run refmac normally it proceeds happily and refines the s

Re: [ccp4bb] conversion from pdb to cif format changes R factors ... why?

That is a serious bug in the deposition task. You can find the refmac command script if you search in the Job list directories. If it does not invoke TLS when there are TLS records provided that is a fixable bug.. Eleanor On Wed, 3 Oct 2018 at 10:51, Antonio Ariza wrote: > Hi Christian, > > > Y

Re: [ccp4bb] How to lift a ligand from one PDB into another

A lot of ways to kill a cat.. Mine: Read in both PDBs - SSM superpose to get the best fit of old over new Then Copy ligand fragment to a new model Merge new pdb and fragment Real space refine fragment save merged pdb E On Mon, 8 Oct 2018 at 09:37, Georg Mlynek wrote: > Dear Nicola, > > Exte

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

I do think at times the Rfree is a bit of a sacred cow . At one level if the maps look OK not much can be wrong.. Is the Ramachandran plot OK? You dont say what the R factor is but does this mean there is a large difference between the Rfactor and Rfree? If you are using REFMAC look at the plots

Re: [ccp4bb] viewhkl : misleading intensity appearance ?

As you say, the two are related but look different, and the intensity on the subsequent images look different too However there are some default scaling parameters, and I have no idea what they are.. Any alternating strong/weak pattern should generate a strong off-origin peak in the native Patters

[ccp4bb] VERY old mtz file..

Anyone any idea what to do about this?? Created in 1992!! Seems unreadable.. No CTYP lines input for file: 1 Indices output even if all data items flagged "missing" Warning, NOT all LABOUT data lines given Warning: Machine stamp corrupted? Assuming native format. >> CCP4 library signal l

Re: [ccp4bb] high B factor

Hard to comment on PHEIX refne but check these things: such results must either mean your molecular replacement solution is wrong or there is something wrong with the data. Refinement packages will always try to match the Mean B factor to the Wilson plot B so I think the problem must be before refi

Re: [ccp4bb] VERY old mtz file..

#x27;s more likely that the programs for reading and writing the > MTZ format changed (and the MTZ format itself changed as well) and are no > longer capable of dealing with "MTZ file mark 1"... > > If I can actually get the VAXes to which I referred to read an old DAT > tape,

Re: [ccp4bb] VERY old mtz file..

You are all extremely informed and clever!! This file is part of an old archive of haemoglobin structures from the 1990s. I suspect they are all generated on a VAX from lcf files when I was "updating" the archive.. So now if I have the character I can update them all again, in the unlikely event

Re: [ccp4bb] RNA pdb molecular weight

There is a CCP4 basic program rwcontents Run it as rwcontents xyzin rna.pdb It lists no_of_C m no_of_O etc.. and sums their mass If you have the H atoms in the pdb that will give you the total mass. If not you will have to estimate the no of H yourself.. Eleanor On Fri, 16 Nov 2018 at 16:46,

Re: [ccp4bb] high SOLVENT content low RESOLUTION and a LIGAND to be found

What is the cell difference? Space group difference- surely not??? Between the two data sets. At lowish resolution the maps can tolerate more cel difference of course than at high resolution.. Eleanor On Wed, 21 Nov 2018 at 13:09, Almudena Ponce Salvatierra < maps.fa...@gmail.com> wrote: > Dear

Re: [ccp4bb] Twinning in C 2 2 21

It is very common for a trigonal spacegroup H 32 to masquerade as C 2 2 21 Here is the log file for other cell. Note that it is possible to reindex it with two cell dimensions equal and a beta angle of 63 - And the self rpotation shows a large rotation at 120 degrees So go back to the data process

Re: [ccp4bb] AutoBuild Invalid MTZ column_types

Looks as though the column types have been run together.. Xia3 writers? It should read "F Q D Q" I believe.. Eleanor On Sat, 15 Dec 2018 at 15:56, Robson-Tull, Jacob < jacob.robson-tul...@imperial.ac.uk> wrote: > Dear all, > > > Has anyone encountered the error "Invalid MTZ column_types for the

Re: [ccp4bb] Survey for the CCP4 community study

potential problems. But this sort of online guideance needs user response too - is it comprehenible? Is it accurate? etc etc. It will be interesting if you can stimulate debate about these issues. Thank you Eleanor Dodson On Mon, 17 Dec 2018 at 19:01, Robbie Joosten wrote: > Hi Marie-Hél

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

Re: [ccp4bb] uniquefy and CELL dimension swap

I think the problem is not in uniqueify but in the GUI implementation. to run uniqueify you need this sort of information SYMM P212121 CELL 10 20 30 90 90 90 RESO 2.3 The GUI helpfully tries to extract the information from an existing reflection file and obviously can get it wrong.. You coul

Re: [ccp4bb] Refmac Question

It is a bit hard to understand why without looking at the structure.. One reason things get disordered is if the occupancies get misset so they add up to a number > 1.0. In that case REFMAC decided this a a "clash situation" and tries to remedy it .. Could that have happened? I build alterna

Re: [ccp4bb] Problem with Rfree and Rfac

The R factor and Rfree will always diverge during refinement; the model is being modified to fit the working set, and not theFree set.. A largish difference at such a resolution is not surprising really. Your rebuilding has improved the FreeR but it isnt surprising thatit has not fallen below

Re: [ccp4bb] Re :Re: [ccp4bb] MAD phasing

You need to try both P61 22 and P6522 with the Se sites changed fron x,y,z to -x,-y,-z. The anom differences can be explained by either solution. But maybe these programs automatically check both hands? Eleanor Dodson Ethayathulla Abdulsamath wrote: hi BertThank you for your reply. Your are

Re: [ccp4bb] Question about twinning

There is something funny visible in the scala loggraphs for the axial reflections. The I/SigI for l=2n are significantly higher than you would expect for systematic absences. You dont say if there is a non-crystallographic translation in your data - the newest 6.1.1 truncate would tell you th

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

Thanks Ian - you have spotted the problem! I believe the Clipper routines must write out as a number the info flagged in the syminfo.lib as number 5 for example ( Spacegroup I 1 2 1) and not the info flagged as: symbol ccp4 4005 There are multiple space groups listed with the same number

Re: [ccp4bb] Possible C2 Twinning

There is a very useful program written by Phil Evans called othercell which gives alternate indexing ( The same functionality is in pointless) In this case it suggests: Alternative indexing schemes which lead to identical or similar cells are grouped on continuation lines if they are symmetry-r

Re: [ccp4bb] [COOT] Novel maps...

, PHFOFCWT (phenix.refine) in addition to the PHIC column of the atomic model. In absence of other phase information, the phase should come from the atomic model, only. Best regards, Dirk. Am 18.06.2009 um 10:24 schrieb Eleanor Dodson: It would be a cock-up map. Unless there is exptl phasing PHDE

Re: [ccp4bb] FW: Molecular Replacement of a small peptide

Have you tried ACORN starting from a random atom? Eleanor Sickmier, Allen wrote: I should have added we are currently getting licenses for direct methods software but right now I do not have that option. Allen From: CCP4 bulletin board [mailto:ccp...@jiscmail.a

Re: [ccp4bb] Migrating R-Free flags across space groups.

If you extend the R32 data set to R3 or C2 you will keep the same FreeeR flags.. You can do this using cad or sftools I think.. Then add those f;lags to your reintegrated data sets.. Eleanor Francis E Reyes wrote: I have an R-free set for R32, I want to try scaling the data into say R3 or C2.

Re: [ccp4bb] RMSD value is different from O and superpose

Are the chains numbered differently? the SUPERPOSE LSQ program requires you to specify which residues to superpose. And any RMS is wildly distorted by a few outliers.. Look at the list of > average differences to see if you have such a problem. The SSM superposition excludes outliers automatic

Re: [ccp4bb] Why NCS doesn't help?

There are many reasons why this could have ocurred. One is that your NCS operator is very close to being a crystallographic one. But you need to give more details of the problem before I can comment sensibly Eleanor Sun Tang wrote: Dear All, In refining my structure (two molecules in au) t

Re: [ccp4bb] space group R32: H settings

As you say there is confusion over R 32 and H32 The pdb coordinate files changed to use H 32 for the hexagonal setting where a=b, alpha=beta=90, the gamma angle =120 The syminfo.lib also uses this nomenclature. However all CCP4 programs (I hope!) check whether the settingis hexagonal or not

Re: [ccp4bb] obtaining a difference of two columns in a mtz file

Arnon Lavie wrote: Hi - I would like to calculate the difference of two columns in a mtz file - specifically of the native and heavy atom structure factor columns. The difference should be in a new column. What is the easiest way of doing this? Arnon sftools will do this. Here is a script t

Re: [ccp4bb] moelcular replacement with large cell

Self rotation is not very clear - and the top peaks are almost certainly generated partly by the high crystallographic symmmetry. Things to check: 1) native Patterson - is there a non-crystallographic translation? ctruncate checks this for you. 2) twinning - if there is a non-crystallographic

Re: [ccp4bb] superimposing Mtz maps

COOT can help you. If you have coordinates in both crystals COt can superpose the coordinates ( LSQ superpose) and carry the density with the coordinates. see under COOT extensions maps Transform maps by LSQ model fit Eleanor Rana Refaey wrote: H

Re: [ccp4bb] Self Rotation map in R32? - trap for young players

It also highlights the problem with looking at plots rather than numbers - there is still a place for them in a graphical age. In one of the molrep outputs - the one confusingly labelled *.doc I think - it lists each peak and its symmetry equivalents. So I guess you would find that peak 1 is the

Re: [ccp4bb] is my crystal twinned or not?

It seems very likely your crystal is twinned - the moments and cumulative intensity are a good indicator of twinning, especially when there isnt much NCS. But your solution is almost certainly partially correct - the Rfactor is pretty low. It is a good idea to run pointless which gives you t

Re: [ccp4bb] how to run detwin?

I guess someone has answered this? Q1 Before detwinning data you must process in the lower symmetry.. Comment. It may not bre necessary or sensible to use detwin - the resukltant estimates of I are pretty unreliable.. You can use twinned data usually to solve an MR problem, and the refine

Re: [ccp4bb] maprot question

I CANT BE SURE of what has happened BUT maprot is a very complicated procedure and your script is trying to do 2 things at once - change the cell and apply the mask. I would try changing the cell first, then generating the mask, then applying it or else: generate mask, apply mask, then change

Re: [ccp4bb] Density modification

Can you send the command script? Eleanor kumar wrote: Dear CCP4¹ers, I¹m trying to run DM for after Refmac on an MR solution but it crashes. I do have the FOM¹s listed in my log file. I get a similar error when I use the mtz file from Phaser¹s SAD + MR. I¹d appreciate any help. Thanks! Kumar A

Re: [ccp4bb] Phase matching program(s)

I cant answer for cphasematch but I believe it uses a resolution dependent phase analysis discussed by Woolfson and Lunin in the 1980s and similar to the method used to calculate the MAPCC used in SHELXE That checks for a possible origin shift as well as analysing difference - but I presume

Re: [ccp4bb] question of extra high B factor

Dont forget the confusing interaction between recorded B factors in a PDB file and TLS parameters. This Q is still I think unresolved but you need to be careful! Eleanor Edward A. Berry wrote: Interesting that the correlation between B-factor and resolution didn't show up in the QDB as recentl

Re: [ccp4bb] Rfree going up

maybe those loops are right - ish. Eleanor kumar wrote: Dear members, I am refining a structure and I notice that when I delete loops that have none, or very little density, the Rfree (which is around 40% at 3.4A) goes up instead of going down. Much of the remainder of the molecule is in good d

Re: [ccp4bb] Twinning

Try refinement with the newest REFMAC which will take twinning into account. But if your integration has missed some spots, or the spots were streaky you may have more complex problems - with what is termed Order-disorder in the lattice. eleanor Rana Refaey wrote: Hi all, I have a few

Re: [ccp4bb] resolution shells for each bin in scala?

Cant you read the shell limits off the loggraphs? The numbers in the tables are given as 4sin**2/Lamba**2 I think but that is converted to As in the loggraph. Is that what you mean though? Eleanor Francis E Reyes wrote: Hello ccp4'ers Where is / how can I obtain the resolution shell for each

Re: [ccp4bb] Making choice on screw axes on resolution with HA sites.

I would expect that if you found HA sites in C222 then they must obey C222 symmetry? Why not just repeat the search in C2221 and see if you get a better answer? Going back a stage: Arent you able to guess whether there is a screw axis from your absences along 00l? Pointless gives a good ana

Re: [ccp4bb] pseudo-translational symmetry

First - there doesnt seem much to worry about. The Rs will be higher than usual when you have a strong pseudo-translation vector. There are many weak observations for the h k l=2n+1 reflections. But in cases like this is is very helpful to force the same indexing on all your different data set

Re: [ccp4bb] pseudo-translational symmetry

Oops - sorry to mislead you. Yes - you are absolutely right.. Eleanor ale...@pasteur.fr wrote: Just a small comment on Eleanor's instructive advices : ... If your original structure has cell (a2= 47.3, b2=58.9, c2=67.6) and angles (alpha2=90, beta2=99.2, gamma2=90) and the second cell i

Re: [ccp4bb] model bias

You dont give the resolution of your data. There are always things to check 1) space group - could it be P222 or P21 2 2 or P 21 21 2 or P2 21 2 etc etc - there are 8 possibilities. You can use absences along the axial lines to help decide on the screw axes, but these can be misleading if you

Re: [ccp4bb] a simple question: how is redundancy measured?

I favour measuring a symmetry related reflection - it is more likely to have different systematic error. But if you after Friedel differences there is some argument for measurng hkl and -h-k-l in the same orientation.. However high redundancy if you can achieve it always seems to me to give

Re: [ccp4bb] refinement with REFMAC5

Debajyoti Dutta wrote: Dear All, I am little curious while refining my structure with refmac5. Each refinement of refmac produces two main files one mtz and one pdb. Will there be any difference with taking the latest mtz vs taking the oldest mtz with the latest pdb. Thank you for your help.

Re: [ccp4bb] space groups not supported by Refmac5

It is Arp waters which doesnt support these space groups I believe.. REFMAC5 seems to accept everything.. And Arp-waters is pretty out of date - cot probably does a better job in positioned fully occupied waters. Eleanor David J. Schuller wrote: For the latter, P21221, you could reindex t

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0 because of the translation so the space group could be P 2i 2 2i or P2i 21 2i But which ever SG it is thedata

Re: [ccp4bb] CNS to PDB format conversion

Manoj Saxena wrote: Hi all, How to convert CNS coordinate file to PDB file format that can be used for refinement in refmac. Is there any utility in CCP4 or other GUI based interface that can convert CNS output file to PDB . Thanks . Manoj Penn Sate University Biochemistry State College P

Re: [ccp4bb] CNS to PDB format conversion

That could be due to anything - a really useless message.. You arent trying to rerun an older refmac script are you - the rerun job button was broken at some point. If you "reset defalt parameters" and then set up the job again it might work.. Eleanor Manoj Saxena wrote: Hi Thanks for yo

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

cted by an analysis of the data statistics. Eleanor Yuan Cheng wrote: Eleanor Dodson wrote: You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0 because of the translat

[ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Yuan Cheng wrote: Eleanor Dodson wrote: This phenonema doesnt necessarily mean you have lattice-tranlation defects - pseudo translations are quite common with perfectly good crystals. Lattice translation defects usually imply your "crystal" has two or more layered different cryst

Re: [ccp4bb] "PDB in" in Refmac5

You need to give a bit more detail.. Here is a plan for MR but you may not have followed it.. there are many ways to kill a pig! 1) get sequence alignment between model and your sequence in astandard format. 2) run chainsaw to edit the model to renumber and rename to your sequence, truncate res

Re: [ccp4bb] Alignment of Electron Density Map for structures that have different space groups

Milya Davlieva wrote: Dear all, I need to make a figure which needs to consist of 2 aligned pdb files and their electron density maps for the structures of two mutants (with different space groups). I'm able to do this when there are two structures that have the same space group. Could, you,

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Ben Ammar Youssef wrote: Hi all, I just want to ask another question related to this topic: Based on the example given by Jerry McCully and if the data has alternate strong and weak reflections, how can we split it into two different files; one containing the weak reflections and the other con

Re: [ccp4bb] electron density slabs

Slabs are almost always due to rogue huge reflection(s). If you run mtzdump on the refmac_output.mtz you will find the maximum value and average value of each column. If you run fft hklin refmac_output.mtz LABI F1=FWT PHI=PHWT then the log file gives you the indices of the largest reflection

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

Rafael Couñago wrote: Hi, I am in doubt between the enamtiomorph space groups, p6522 and p6122. Is there a way to distinguish the correct one in the absence of a molecular replacement model? Cheers. Rafael. No is the short answer.. If you have heavy atom data with anomalous scattering yo

[ccp4bb] sorry

Oh dear - Apologies. I sent the ctruncate filre to the whole BB - maybe you SHOULD all update the distributed one from 6.1.1 but I didnt mean to do it that way.. Eleanor

Re: [ccp4bb] Low Bfactor values for waters after TLS

Yes - I have had a similar problem.. We need a reply from Garib.. Eleanor Alasdair K. Mackenzie wrote: Greetings CCP4-ers, I have been running some TLS refinement which does wonders for my R/Rfree values, but seems to give some spurious Bfactors/ADPs for the waters, e.g. B= 2. These low Bfa

Re: [ccp4bb] Strange Merohedral Twin result

Neha Kharbanda wrote: Dear All, I submitted my processed.hkl file to the Merohedral Twin server and the results are bit strange the curve corresponding to my data goes below the perfectly untwinned red line..the complete opposite of the theoretically twinned red curve line. Has anyone

Re: [ccp4bb] backbone b-factor

Choose another graph from the loggraph - it also gives the main chain alone and the side chains alone (not so useful!) Eleanor Salameh, Mohd A., Ph.D. wrote: Dear All, I would like to prepare a plot showing the b-factor of only the alpha carbon and/or the backbone atoms and I wonder if somebod

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

I would like to have some comments on whether the maps before or after truncation are better . (obviously the Rfactors will be lower for the truncated data ..) I suspect it iwill be completely anecdotal - but I confess to a gut unhappiness about throwing out measurements.. eleanor Pavel Afon

[ccp4bb] a relacement for watertidy?

There is a useful, but out-of-date program in the CCP4 suite called watertidy. it analyses the H2Os and after applying symmetry to move them close to the protein, relabels them according to the protein atom they are closest to So for protein chain A you can output a water chain W where the W

Re: [ccp4bb] perfect twin test

Such anomalous /*2 values usually reflect the fact that you have a non-crystllographic translation which means a large % of your reflections will be very weak ( eg if you had mistakenly called a C2 data set P2, all the h+k=2n+1 would be ~0, and non-crystalllographic translation can cause simila

Re: [ccp4bb] Rfree in similar data set

Mike England wrote: Hi all, I will appreciate your comments on the following case: I have two datasets from the same or identical crystals. Initially, I refine a structure against the first data set and later on switch to another dataset for further refinements. Do you think, my Rfree will be

Re: [ccp4bb] Contact Surface Area

Daniel Bonsor wrote: I am trying to calculate the contact surface area of a loop. Using ArealMol I only get the overall contact surface area per residue. Is there any way to get it per atom or does anyone know of a program (online/software) which will perform this task. Thanks in advance Dan

Re: [ccp4bb] taming structural biology

I like the David Blow book very much Outline of Crystallography for Biologists /by David Blow / And there is another good one by Jan Drenth.. Eleano Katja Schleider wrote: Hello everyone, I am no structural biologi

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

It is hard to believe that REFMAC is being driven by rotamer conformations - REFMAC weighting scheme gives a low priority to fitting a preferred rotamer - quite rightly since the SD on rotamer angles is high. The ideal is only "ideal" for a residue in a near vacuum - the interactions with othe

Re: [ccp4bb] MOLREP

How can that be! Are you also providing a sequence? Eleanor Tommi Kajander wrote: Hi, I have been using a dimer as a search model in MOLREP (there will be several in AU), for some reason the program tends to break the dimer into monomers wihtout asking me.. how is this determined in the prog

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