Re: [ccp4bb] About system absence in P4222?

routines). Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson Sent: 15 December

Re: [ccp4bb] Transferring a Free R set.

Alun R. Coker wrote: Hi All, I have been in the habit of transferring my initial free R assignments to any new data sets or to isomorphous data sets such as substrate complexes. Although theoretically this is necessary to obtain a valid free R many of my colleagues maintain that this is

Re: [ccp4bb] Refmac and MSE?

I also see such peaks. I have assumed it is because the default in REFMAC is to use the CuKa SE formfactor, which should be modified at shorter wave lengths. (Solution - copy $C:IBD/atomsf.lib and modify Se c to c(CuKa) - f' for your wavelength.. then assign ATOMSF myversion/atomsf.lib in the

Re: [ccp4bb] MR- Problem-76 % seqeunce identity-no solution

Meetmr Ss wrote: Dear all, I struck with MR problem. MY target has 76% sequence identity with the model. I tried Phaser, AMoRe and Molrep. None of them gave me satisfactory solution. If you have any suggestions and or New programs I would like to try. Thanks somu Is your space

Re: [ccp4bb] NCS restraints of domains

It is worth doing sme rounds of non-NCS restrainded refinement then sending it to the Ethan Merrit server to get TLS groups suggested.. Eleanor Frank von Delft wrote: Two points: 1. B-factors tend to differ lots between NCS copies, so you want to set those restraints rather low (at least, I

Re: [ccp4bb] Secondary structure restraints

Phil Evans wrote: Does anyone have a good way of imposing secondary structure restraints in a low resolution refinement? I've done this in the past as hydrogen bond distance restraints within helices, input to refmac as LINKs , with the list generated with a little program and certain amount

Re: [ccp4bb] Ramachandran plot, in a text list

John Pak wrote: Hi, sorry if this was posted earlier. How can I calculate a Ramachandran plot, but output the information to a text file list? i.e. something like Ala51, phi=X, psi=Y. I can't seem to find this information in the ccp4 SFCheck/Procheck log file. I thought PROCHECK listed

Re: [ccp4bb] Problem during refinement

One possibility is this: By default, REFMAC decided something is a cis-peptide if the omega angle is 90.0 . It also reads and believes any CISPEP records you have in your input pdb. (You can turn this feature off by requesting REFMAC to only restrain to a cis peptide if you have a CISPEP

Re: [ccp4bb] difficult MAD dataset

With a pseudo translation vector like that the SG could be any of the 8 orthorhombic SGs; P222 P21 22 P21212 P212121 P2 21 2 P2 21 21 P 2 2 21 Test them all, and see if any give a dect solution.. Eleanor Alison Li wrote: We recently collected a complete 2.5A MAD dataset. However, finding a

Re: [ccp4bb] Fobs - Fobs

Rana Refaey wrote: Hi, I was wondering if anyone knows what programme I need to use to subtract the Fobs of two different crystals from each other. Regards, Rana _ Invite your mail contacts to join your friends list with Windows

Re: [ccp4bb] Obtaining relationships between two cross rotation solutions?

I presume theta1 theta2theta3 are eulerian angles? When theta2 ~ 0, you can onlyy define theta1+theta2 so solution 1 is effectively the identity; theta1+theta3 = 360 (ie 0) theta2~0. theta3 not defined - that generates the identity matrix. When theta2 ~ 180, you can onlyy define

Re: [ccp4bb] Choosing MR solutions in the case of perfect twinning with P41212?

Points to think about. 1) Do your data statistics indicate twinning - if they dont iyt is mst unlikely to be present Look at output of truncate ( new Ctruncate is better) Get phenix xtriage report.. 2) SAD phasing - I presume you knw it is P41212 and not P43212? 3) Going to a lower

Re: [ccp4bb] PHIDM AND FOMDM from DM

Xie Jiabao wrote: Dear all, I am using the density modification tool in ccp4 to generate improved phases for/from my model. I find that the electron density map I generate using Fobs, and density modified phases (PHIDM) are not the same as that generated using Fobs, phicalc (original

Re: [ccp4bb] refinment of mir anomalous data in MLPHARE

What are you assigning as FP and FPH? Can you send the complete command script? You have set a real occupacy to 1.0 which is not appropriate if FP and FPH are equal - it should be 0.000 But I await you complete script.. Eleanor Alpharyun Ni wrote: Hi everyone! I have a problem when I use

Re: [ccp4bb] unstable refinement

You dont say at which point in the refinement cycle you are.. The refinement algorithms are meant to reduce these parameters, and if they diverge wildly there is probably something seriously wrong either with the software or the model.. eg - different cell dimensions or space group for the

Re: [ccp4bb] Refinement

More details? Are there any particular data problems ? Is twinning a possibility - look at new truncate plots.. Eleanor Rana Refaey wrote: Hi all I have two datasets of resolutions 1.6 and 1.65 Å both of the same molecule, the problem that i am facing is the refinement. The R factors are

Re: [ccp4bb] Twin refinement - selecting FreeR Q for Garib..

Is it true that when doing twinned refinement REFMAC does not use the assigned FreeR set? Eleanor Roberto Steiner wrote: Hi Sabine, If your question is: Is it possible to refine twinned structures with Refmac? My answer is: Yes. Very well. Best wishes, Roberto On 20 Feb 2009, at

Re: [ccp4bb] Wilson B-factor from truncate

I am a bit confused - my graphs have the X axis labelled in As? but are you looking at the actual numbers? For me the log files have the label $$ 1/resol^2 obs all $$ 1/resol^2 does equal 4 sinsq/lamdasq The output fits this equation: ie K and 2B are determined for the intensities;

Re: [ccp4bb] TLS refinement in Refmac gets stuck

Yes - I found that irritating bug; it is a disaster for less experienced users.. It doesnt seem to happen with the linux installation.. Eleanor Anita Lewit-Bentley wrote: Hi Ian, A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you

Re: [ccp4bb] 3ftt and gremlins

It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor Wladek Minor wrot Dear All,

Re: [ccp4bb] Could I improve an inconsecutive experimental map?

I presume you have done density modification after calculating the exptl phases? If you use REFMAC to refine your partial model with the exptl/density modified phase restraints your FWT PHWT fourier coefficients already use the combined phase. I am not sure how to choose a damping factor. If

Re: [ccp4bb] images

, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show

Re: [ccp4bb] Twinned data and maps

I am not sure if there is any way of avoiding model bias if the coordinates are included regardless of whether there is twinning or not - my preferred method is to set the occupancies of suspect regions to 0.00 then do refinement of the better parts of the model and then check maps again and

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned

Re: [ccp4bb] map coefficients for padded reflections Fobs=absent

To add to Garibs answer - it is a good idea if your data set is pretty complete - but can enhance model bias if it is not . Eleanor Garib Murshudov wrote: On 18 Mar 2009, at 01:47, Bernhard Rupp wrote: I mean *absent* reflections here with fobs=0 Dear All,

Re: [ccp4bb] nad woes

Even for NAD I think I would make my own new dictionary. If you go to the ebi site ( now pdbe) ask for Msdchem ( is it PDBeChem now?) Get the idealised NAD coordinates with the remediated nomenclature Submit the coordnates to the ProDrg server. Retrieve the REFMAC dictionary Use PDB and

[ccp4bb] refmac not rerunnable

This is VERY VERY VERY irritating! Why has it been allowed... Is there any advantages?? Eleanor#

Re: [ccp4bb] two identical proteins in one asymmetric unit

Sang Hoon Joo wrote: I am refining my crystal structure in which I have two identical chains in one asymmetric unit. Space group is H32 and each chain yields me a biological trimer as expected. The problem is, do I have to assume they are identical, or they are really different. After each cycle

Re: [ccp4bb] Differences in Refmac5 refinement on CCP46.1.1

Before worrying at the rmsbonds check whether you have some significant outliers - these would be listed in the REFMAC log file. Sometimes these can really distort the quoted values. Eleanor Anastassis Perrakis wrote: Hi Rafael, Things very different on the new version: - The rmsANGL

Re: [ccp4bb] I/sigma continued

I agree absolutely with James - be as succinct as you like in a table but include the verbose definition for each entry in the log file - or at the very least in the manual. It should be easy to search for with the table tag. People will not go and read a reference.. Eleanor James Holton

Re: [ccp4bb] Cross-crystal density averaging and/or refinement

Have you tried DMMULTI? It can do a brilliant job.. Eleanor Ethan Merritt wrote: Hi all, I have an interesting problem case at the moment. We have crystallized the same 2-domain protein in two different, i.e. non-isomorphous, crystal forms. There is a decent homologous structure for one

Re: [ccp4bb] Rotation angle and translation distance

LSQKAB gives something of what you want.. If you fit domain_open to domain_closed after the rest of the structure is aligned. you get the COM of the two domains. the rotation angles in euler and polar form I would say the rotation angle was the omega angle and the translation the difference

Re: [ccp4bb] predicted secondary structure based alignment

The PISA service at the EBI does exactly this msdpisa Either download a pdb or use the CCP4 GUI to run a cut down version of it in house Eleanor Kay Diederichs wrote: Hi, check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Servers_and_programs_for_sequence_analysis

Re: [ccp4bb] good phasing, bad R-factors

Well - some things to consider. 1) Rfree will often go up a bit but this seems too much. 2) Does the mz file have the right spacegroup in the header? It is possible to have processed data in one spacegroup and have the Se solution in the enantiomorph.. You might have to actually CHANGE the

Re: [ccp4bb] Reindexing Orthorhombic

Mo;lecular replacement can choose any suitable origin so you cant predict. The easiest way is to run superpose molecules Match all residues to each other. You should get a rotation matrix -1 0 0 0 0 1 / 0 1 0 with some translation which sjould be very c;lose tpo components of 0, or 1/2 along

Re: [ccp4bb] Help needed in solving a MAD dataset

Minor correction: SHELX software are not part of CCP4 but if you have them installed as part of your crystallograhic software, you can call them from the CCP4 GUI. You can obtain the SHELX suite free to academic labs from Ggeorge Sheldrickbe Email George Sheldrick. George M. Sheldrick

Re: [ccp4bb] translational NCS

pdbset xyzin mol1.pdb xyzout mol1-tran1.pdb SHIFT frac x,y,z (where x,y,z is the patterson peak) end OR pdbset xyzin mol1.pdb xyzout mol1-tran2.pdb SHIFT frac -x,-y,-z (since -x,-y,-z is also a the patterson peak) end Nicolas Soler wrote: Dear CCP4bbs, I am dealing with a case involving

Re: [ccp4bb] Translational pseudosymmetry?

This looks a bit strange.. If you have a hexamer in the asymmetric unit, in P3, then that means all symmetry copies lie in the same plane. To generate the Patterson peak, 2/3,1/3,0 the hexamer must be centred at 1/3,1/3, z (with symmetry equivalents 0,-1/3,z and -1/3,0,z ) I would expect

Re: [ccp4bb] molecular replacement

Hmm - that is odd. You may have the wrong SG in the mtz file. Try MOLREP or PHASER with the option to try all spacegroups consistewnt with the pointgroup. Eleanor intekhab alam wrote: Hi all I am trying to do molecular replacement with low resolution (4Å) using Molrep and Phaser. Overall

Re: [ccp4bb] Alignment software

Salameh, Mohd A., Ph.D. wrote: Dear All, I'm trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd We found esprit very

Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?

If you ask for Real space R factor from overlapmap it gives you the mean density for eaxch residue main chain and side chain, or mean density at atom centre. It is rather confusedly labelled Fobs(mc) etc. You could convert this to sigma level by just dividing the values. Eleanor The

Re: [ccp4bb] Finding best model for molecular replacement

Some afterthoughts: Of course avoid the common MR problems - assigning wrong SG, saturating low resolution data etc etc.. 1) Any sequence search tool might have told you there was only a poor match available. 23% is very marginal for MR and with that degree of similarity you are very wise to

Re: [ccp4bb] Structure Based Sequence Alignment

Muhammed bashir Khan wrote: Dear All; Can some body tell me a website for structure based sequence alignment, which can also pin point the similar and identical residues in different colors. regards Bashir PISA does just this - go to the ebi web site and select pisa

Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi,

Re: [ccp4bb] How to calculate real-space CC by section?

If you ask for CORR SECTion then overlapmap does just that - the CC will have a certain value for each section regardless of the CHAIN parameters. If you want correlation residue by residue you must ask for CORR RESI As someone said - a lousy model will give poor CCs even if the map is

Re: [ccp4bb] How to calculate real-space CC by section?

I havent a reference for the correct value of the CC - it is just based on maps I have seen solved then checked out later. but if your final model gives a very poor CC with a map calculated from experimental phases, either for parts of the structure, or for the whole, it is time to worry.

Re: [ccp4bb] How large should the real space correlation coefficient be?

Maybe it is worth recalling some ancient discussions, involving Real Space R factors as defined by Alwyn Jones and Gerard Kleywert. If I remember properly, they give an Rfactor between the density in an ATOMMAP generated from a model, but with truncated B factors and the density in the map

Re: [ccp4bb] The Total CC in the output of CCP4 OVERLAPMAP

You are in luck - it is the total CC over all grid points used for that Table Eleanor Hailiang Zhang wrote: Hi all: Thanks for all kindly helps with real space CC. Now I have a new question again. In the output of OVERLAPMAP in CCP4, there is a almost last line saying Total...:

Re: [ccp4bb] How to align a sequence to a know profile

chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG

Re: [ccp4bb] Ligand present in only one monomer in NCS

The rnase structure used as the $CEXAM for CCP4 is another example - a typical coordinate set is 2sar.pdb There one monomer binds the substrate very clearly, whilst the other is blocked by crystal contacts. Eleanor ANDY DODDS wrote: Hello, I am solving a structure of an enzyme, which

Re: [ccp4bb] About solvent flattening

Oh dear - I havent used SIGMAA for a long time . If you use REFMAC to calculate your SFs then it generates FC PHIC and FOM in the output. That is the easiset approach to getting started.. Isnt there a GUI task to do just this? Eleanor Hailiang Zhang wrote: Hi, I wanted to do solvent

Re: [ccp4bb] About solvent flattening

One or two more comments. There is a later paper by Andrew Leslie showing that the WANG real space averaging can be carried out very simply and much faster in reciprocal space - and this is the method used by all subsequent programs. density modification using calculated phases is somewhat

Re: [ccp4bb] Fwd: creating a metal plane model to fit a protein.

Well - try the coordinate utility recommended by Martyn Winn to convert cif to pdb coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb eof END eof Then pdbset xyzin 1ivo.pdb xyzout 1ivo-sym.pdb symgen -x,y,z (or whatever sym op you want) end This will generate symmetry copy of your coordinates as

Re: [ccp4bb] MR on low resolution soaking data.

The easy Q first: Wilson plot B values are very unreliable for 4A data - b=20 is almost certainly wrong, but until you have a model to refine it is hard to get a proper estimate. Q2: With a decent model the ligand should show up as a blob, even at this resolution. You might have trouble

Re: [ccp4bb] JLigand Coot link

This is a REAL PAIN Paul! Eleanor Debreczeni, Judit wrote: Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED.

Re: [ccp4bb] sketcher

Can you send your fragment of the pdb containing the ligand, and the cif file? Eleanor Yahui Yan wrote: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered

Re: [ccp4bb] JLigand Coot link

But does it follow the PDB format for LINK records; it is a disaster if the LINK read from the PDB have a different definition and information content than LINK records output from REFMAC. At least LINKR is a flagged non-standard record. Eleanor Garib Murshudov wrote: In the latest, latest

Re: [ccp4bb] Stuck refinement

When this happens, I firstly suspect that the spacegroup may be wrong. We had a case where the symmetry was pseudo I4212 but was really I222 (or was it really I212121) Anyway most of the structure obeyed the I41212 symmetry but there was a tail which did not..) Feed the unmerged

Re: [ccp4bb] Multiple NCS relations

If this is happening something is wrong! REFMAC can certainly use multiple NCSR requests.. I usually check the agreement with the Superpose molecules task (Coordinate utilities) matching all atoms just to make sure that AC does match A'C' and B matches B'. If the RMS difference is greater

Re: [ccp4bb] model refinement (corrections, apologies!)

Rfactors can vary a lot for equally good results it seems. You need to look at your Rfactor v resolution to see if there are any problems - ice rings? low resolution stuff? etc etc Have you used TLS sensibly - this can help.. etc etc But if the maplooks good you should be happy. Eleanor Tim

Re: [ccp4bb] f2mtz error: problems reading reflection

Can you attach the first 50 lines of your hkl file? Eleanor Yogesh Gupta wrote: Dear Experts, After a new installation on Mac OS 10.6, i am getting this error (related to f2mtz) during the Find SITES step by SHELX in Autosharp. Data line--- LABO H K L FA SIGFA ALPHA Number of columns to be

Re: [ccp4bb] Fast,medium,slow axis do not match

Alternatively you can force the fft to generate a map with the sfall axiis order (sfall has a fixed axis order governed by the spacegroup) From the fft documentation You can set AXIS fast medium slow Eleanor Kevin Cowtan wrote: You could feed *both* maps through mapmask with AXIS X Y Z to

Re: [ccp4bb] Programs to detwin.

Hmm - detwinning is difficult - problematic , because you need to give a fixed twin fraction, which you may have estimated wrongly. both SHELX (I think) and REFMAC (I know) will refine with multiple twin operators, improve the twin fraction estimates, and output an fobs which is a detwinned

Re: [ccp4bb] Calculate the portion of the density within a mask

mapmask will do this. Eleanor See the documentation - it is a bit confalued but certainly works.. Hailiang Zhang wrote: Hi, I want to calculate the portion of the noise density with respect to the whole unit cell (assuming the model is good enough). I plan to first calculate the integral

Re: [ccp4bb] Twin questions: is my crystals twinned or not?

There isnt much evidence for twinning that I can see. Moments sensible, Ltest sensible for untwinned data, some distortion of the cumulative intensity plot but that could be due to integration problems. Comparing Rfree in P3 is only proper if you have kept the same FreeR set as you assigned

Re: [ccp4bb] A strange case of MR

Have you used pointless to examine possible spacegroups? It is possible to get one lattice point out and get a very high rsym pointless will check these possibilities for you The cell could be this: C m m m 39.6 149.9 18.2 89.9 90.0 90.0 0.10 [-k,-k-2l,h] You need to go back to

Re: [ccp4bb] differences Rfactor calculations

Everything said is true, but one of the most important factors in calculating structure factors and hence Rvalues is the scaling and solvent model. All of these are pretty inadequate - probably all protein crystals have large volumes of multiply ordered atoms - water networks, alternate

Re: [ccp4bb] FT of fo-fc.coeff

i dont think you are tackling this problem in the simplest way. as boaz suggests, you can use phaser to find several molecules, either several copies of the same model, or first one type of model, then a second. The CCP4 GUI interface guides you into how to do this, you input ensemble1 ( first

[ccp4bb]

MR may work - it is worth a trial. Are you sure the SG is P622 or could it be P6i 22? You can check al these with MR and hope to get a much better result in the correct SG Eleanor Vandana Kukshal wrote: hello sir , recently i have collected one data of 3.0 A of a protein having no

Re: [ccp4bb] chainsaw with multiple chains

Sorry - i dont know the answer but why dont you divide the pdb into two parts, ditto the pir alignment and run two chainsaw jobs? Clumsy but it should work.. Eleanor Ronnie wrote: If i want to use chainsaw to prep a pdb file that contains two chains of different sequences, how do I format the

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Just adjust the scale parameters in the FFT script - mF1-nF2 option. Eleanor Armando Albert de la Cruz wrote: Does anyone have got a script to compute 3fo2fc map with CCP4? Armando El 29/07/2010, a las 23:38, Ian Tickle escribió: On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine

Re: [ccp4bb] Does phenix have any utilities which can do B-factor sharpening?

Hailiang Zhang wrote: Hi there, Does phenix have any utilities which can do B-factor sharpening (with user-specified Bsharp values) when calculating maps? Thanks! Best Regards, Hailiang You know you can do this in coot on the fly, and test different Bs visually? Eleanor

Re: [ccp4bb] cphasematch

Should work if you have the same indexing convention.. Another of Kevins utilities; csymmmatch -pdbin old.pdb -pdbin-ref SADbuild.pdb -origin-hand will compare the two models, and correct for symmetry and alternates due to reindexing I believe.. Eleanor wtempel wrote: Dear colleagues,

Re: [ccp4bb] To view the 2mFo-DFc map generated by SIGMAA

Actually I think it needs the labels FWT PHWT I may be wrong but like REFMAC I think it outputs a ositive FWT and PHWT is either equal to PHIC or to PHHIC+180, depending on the sign og FWT = (2m|Fo| - D|Fc|) Eleanor Hailiang Zhang wrote: Dear Tim: This is also what I thought. Thanks!

Re: [ccp4bb] calculating solvent volume from molecular surfaces

Alastair Fyfe wrote: Does anyone know of software that will segment a unit cell into volume internal/external to a calculated molecular surface ? thanks! Alastair Fyfe Well, if the surface was generated from some sort of model it is easy to mask the unit cell map to set all the volume

Re: [ccp4bb] PEG in the pdb? zero occ

I agree that zero occupancy is a bit ugly, but useful when not sure whether you will ever see that LYS.. But I dont think it wlll displace bulk solvent - at least not in REFMAC where an atom with occ=0.0 will not contribute to the atom map. And I expect this is true for all other structure

Re: [ccp4bb] Can I refine the B values only for the modified/added structure while keeping already refined B values unchanged?

I really dont think this is a very good idea - B values are correlated to the optimum position of the atom - if thast is a fraction of an A out the B factor will be much higher than it should be.. Eleanor Hailiang Zhang wrote: Dear Pavel: Thanks a lot! I will try phenix.refine! Best

Re: [ccp4bb] atomic B factors

That must be a bug.. 2.00 is the lowest value permitted . Possble causes: You have very low resolution data, and the overall B value is badly estimated (not very common) common cause: you have done TLS refinement which reports b value differences from the TLS derived values. If you start

Re: [ccp4bb] rigorously compatible coordinate files

In fact the old PROCHECK which is still distributed with CCP4 I think does it - I am not sure that it obeys any current PDB criteria, bur it will give you two matching files. Eleanor James Stroud wrote: You seem to have two different criteria listed, one more general than the other: 1. You

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Well - that is exactly what COOT does isnt it? Eleanor Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards,

Re: [ccp4bb] ? steps after detwinning

Seema Nath wrote: my crystals have 0.401 alpha-twinning fraction,which on detwinning reduced to 0.22 also pseudo-translation ~48.5,the resolution is poor,3.7 angstorm,please suggest next step after detwinning thanks in advance .. Sorry to be flippant, but you would probably be best

Re: [ccp4bb] DM NCS averaging question

The commonest error with averaging is getting the mask wrong. Check that the CCs after application of the averaging start at a reasonable value - 0.3 at least and increase with each cycle ( by the way why do ncycle 1?) But in the end the density will not be identical, the Fobs are not

Re: [ccp4bb] DM NCS averaging question

Well - if the CCs are 0 then no averaging can take place. You know you can let DM make the mask itself - are you using the GUI? It shows you what to set.. Eleanr zhan...@umbc.edu wrote: Hi, Thanks for reminding me checking the mask. I think their might be something wrong with the mask,

Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?

Remember you need to look at half the contour height in a mFo map compared to a 2mFo-DFc map - the same domain should show up but at a lower relative contour level in both maps. REFMAC calculates a similar WCNG and you can look at the graph of m after refinement to see how close it is to 1.

Re: [ccp4bb] protein dimensions

pdbset gives it to you too. pdbset xyzin a.pdb end if you want the principal exes I still use Amore table function - that reorientates the model according to ppl axes then gives you the dimensions along each axis.. Tim Gruene wrote: On Wed, Sep 08, 2010 at 08:21:33PM +0200, Nikos Pinotsis

Re: [ccp4bb] non-identical complexes in the asymmetric unit

I use PISA to analyse this - sometimes the differences depend on the definition of what is a hydrogen bond? and unless you have very high resolution it is risky to say there are significant differences.. But certainly there are examples where the results are very significant indeed - you could

Re: [ccp4bb] Molecular replacement question

Does your model structure form a dimer? Maybe best to search with that model.. eleanor Paul Holland wrote: Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very high sequence similarity to the search model with several predicted

Re: [ccp4bb] ? steps after detwinning

Do you have translational pseudo symmetry - what is the evidence? It can confuse space group assignment.. Eleanor Seema Nath wrote: After running phenix.xtriage the possible point group is P622 and possible spacegroups are P622,P6122,P6522,P6222,P6422,P6322. Using this information when I run

Re: [ccp4bb] Difference map

That seems the right procedure. I presume the two crystals have similar cell, etc? What is the Riso plot from scaleit look like - if it is 55% + then there is no isomorphism, but if it is 30% then the map should be reasonable. which phase did you use for the map calculation? Eleanor

Re: [ccp4bb] 'ERROR' in merging two data sets

Different numbers of columns wont stop CAD working, but if you have the any occurence of the same labels in either file this will produce an error mesage - eg Label FreeRflag found twice.. And if you have labelled both data sets as Fnew or some such uninformative label, then again you will

Re: [ccp4bb] changing spacegroup

Or mtzutils hklin1 a.mtz hklout b.mtz eof SYMM P43212 eof Graeme Winter wrote: Hi Tim, Is it as easy as reindex hklin a.mtz hklout b.mtz eof symm P43212 eof This will simply (and correctly) reassign the symmetry operations. Is this what you meant? Best wishes, Graeme On 30 September 2010

[ccp4bb] T N Bhat

Does any one have T H Bhats email - He was at RSCB I think but is probably retired. Eleanor

Re: [ccp4bb] mol rep help needed

Suggestions: Are you using the GUI - that gives you a molrep option to provide a fixed model.. Re Amore - yes you can do this - run first pass as autoamore which should find one monomer, the keep on redoing the TRAN fun providing the solution to 1st, 1st+2nd, etc as known solution - all

Re: [ccp4bb] R factor R free struck

1) Rigid body refinement wont reduce R factors much more than this - start restrained refinement with NC restraints.. 2) And yes - at low resolution you could expect a large difference between R and rfree 3) With such high NC symmetry is there any possibility of another SG? Eleanor Jack

Re: [ccp4bb] R factor R free struck

Is that necessary? Eleanor J. Preben Morth wrote: hi remember to reindex your data to P21212 in case you used Phaser to search all alternative orthorhombic SG's and it found P22121 Preben On 03/10/2010, at 04.56, Jack Russel wrote: Hi all, I have collected a data at 2.9 Å and the solved

Re: [ccp4bb] I really need a file(such as .pdb) contains pseudo tanslation

Well - here is one example, but there will be many more Try 3pva.pdb As for this problem: (I also can't convert mmCIF to MTZ using cif2mtz) Can you give an example? That should be fixable.. Eleanor On 10/12/2010 10:19 AM, Ting-Wei Jiang wrote: Dear all For a particular purpose, I have to

Re: [ccp4bb] Fwd: [ccp4bb] Fill map/mask with dummy atoms?

Doesnt arp/warp start with doing something like this? If you gave a 0/1 mask I wonder what the first build would look like.. You would have to invent a reflection file for the map ... E On 10/13/2010 12:49 PM, Dirk Kostrewa wrote: ... maybe, to clarifiy my question a little bit: I want to

Re: [ccp4bb] cad, freerflag, uniqueify : free set when making anomalous from merged data

To try to answer the Q I think you are asking.. If you keep anomalous seperate you will get a file from ctruncate with h k l F+ SIGF+ F- SIGF- I+ SIGI+ I- SIGI- The observations flagged as F- or I- etc are actually measured for the reflection -h-k-l So uniqueify generates markers for

Re: [ccp4bb] Reindexing scaled data

You dont need to reprocess - just reindex k,l,h or whatever you want to do.. Reprocessing is not necessary if you are keeping the same pointgroup. There is no change in the expected geometry of the diffraction.If for example you were changing from pontgroup P222 where all angles are restrained

Re: [ccp4bb] Refinement

On 10/19/2010 12:39 AM, Jyotica Batra wrote: Hi All I have a dataset at 1.9A, spacegroup-P212121 (unit cell: 37.7, 39.52, 231.72, 90, 90, 90), I used MR phaser and got a structure solution with LLG= 320 (1copy/a.u) . During refinement, the R-free (50%) and R-factors (42%) never go down. I

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