Re: [ccp4bb] refmac5 issues: C-terminal amidation and maltose library file

Q2 Copy the MAL entry into your own directory cp $CLIBD/monomers/m/MALcif ./ Then correctt it in your directory And assign LIBIN ./MAL.cif The program will read your corrected version and ignore the distributed one. Q1 If you run REFMAC the GUI under review restraints, it will detect and

Re: [ccp4bb] Problems in refinement with NCS and B-values

If you have used TLS the B factors listed for the residues are the residual values AFTER the TLS is applied so they are correctly restrained to be quite close - the differences in the molecules should be expressed in the hard-to-visualise TLS parameters. The first check is to run TLSANL and as

Re: [ccp4bb] low b factors

Are you using TLS? If so the B factors in the PDB file are relative to the TLS parameters.. Or have you lost low resolution data - you can see that in many plots - one in REFMAC gives v as a function of resolution? If so you probably need to use SCALE SIMPLE - in gfact that is usually the

Re: [ccp4bb] phenix mtz to ccp4 mtz conversion

REFMAC expects F not I so you need to convert the file.. You will need to run TRUNCATE to convert I to F or the GUI task under Data processing Eleanor John Bruning wrote: Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs

Re: [ccp4bb] High Wilson B

It is hard to get a resonable estimate of Wilson B with 4.5A to 3A data, but yes - if the crystal stops diffracting at 3A that seems reasonable to me Eleanor Michael Colaneri wrote: Dear colleagues, I have a B of 75A**2 from Wilson statistics 4.7 to 3 A res, good straight line. Has anyone

Re: [ccp4bb] initial model built in Fo map not refining

Does the mtz file you are using for refinement have the correct spacegroup in it? Sometimes it gets left as the pointgroup P222 and causes disasters (you just need to run mtzutils hklin1 now.mtz hklout x.mtz SYMM P21212 end Eleanor Satinder K. Singh wrote: Hello, I have a SAD data set to

Re: [ccp4bb] initial model built in Fo map not refining

The new pointless which is the underlying program for the "Test Alternate Indexing" task from the CCP4-6.0.2 GUI works brilliantly for matching 2 data sets. However in P21212 if a not-equal b not-equal c it is hard to confuse them.. Like Tassos I think you should start your experiment by mergi

Re: [ccp4bb] struggling with molecular replacement

Does your cell show pseudo symmetry or NCS translations? Eleanor Wu, Mousheng wrote: hi, everyone! I am struggling with my crystal structure in a very big unit cell. my protein is about 16KDa. probably there are about 20 molecules in the asymmetric unit. I tried to use molecular replacement t

Re: [ccp4bb] Problem converting CNS cv file to mtz using f2mtz

CNS format changes with the time of day and unfortunately f2mtz requires that you give a correct fortran format stt. This command script works from the GUI: Note that 1) you must the "skip lines" 2) you need X entries to skip unwanted characters . These include INDE (7x) FOBS= (6x) and also

Re: [ccp4bb] pseudo-translation vector in molrep

I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01 but it must be too close to the origin to be a translation vector from one molecule to another. There are reasons for such peaks - sometimes spurious large terms in the data.. but they dont usually represent true molecula

Re: [ccp4bb] how to bring back the missing density for half of the structure

There are many many kinases with different conformations of the C terminal and N terminal domains. I would first refine the Cterminal as far as you can go - correct the sequence etc etc. Then align a selection of kinases on your C-terminal coordinates ( MSDfold at www.ebi.ac.uk/msd will return

Re: [ccp4bb] difference density ripples around Hg atoms

Well - there will be a ripple, but is it there in the difference map as well? that is meantto be less affected. REFMAC5 claims to be able to refine some atoms anisotropically and that would be a good place to start Maybe you will need to read the documentation! There is some way of request

Re: [ccp4bb] stacking interaction!

Try submitting your coordinates to www.ebi.ac.uk/ msd and choose the task MSDpisa It gives you lots of info including that.. Eleanor Sreeram Mahesh wrote: Hi All! I have found stacking interaction between aromatic residues of a structure of an enzyme. does anybody knows any server which

Re: [ccp4bb] Tweaking with SCBUlk and BBULk parameters in refmac

Well - this (expert??) would suggest using SCALE SIMPLE - SCBULK is a fudge which has some theoretical justification if you have measured very complete and accurate low resolution data, but seeing most people havent done this it remains a fudge factor The justification is related to average s

Re: [ccp4bb] Calculating vertical offset of helices

Jie Liu wrote: > Dear CCP4ers: > > Does anyone know an existing program to calculate the lateral > displacement---the vertical offset, measured as a fraction of the > the heptad repeat---of neighboring helices in coiled coils or helix > bundles, either parallel or antiparallel? > > Your input is g

Re: [ccp4bb] CCP4 mailing list

Well - I seem to get many things twice! Prob. my fault - and it fills up my "Deleted" box.. Eleanor Thomas Stout wrote: Has anyone else noticed that they're only getting some of the postings on the CCP4 mailing list? Lately I've been noticing that I often see responses to queries, but n

Re: [ccp4bb] Merging datasets

There might be many reasons.. Do you have a spacegroup with alternate indexing? If so the two crystals may not be using the same convention. See $CHTML/reindexing.html for more details. Or is one data set a high resolution pass and one a low resolution pass? Sometimes then there are saturated

Re: [ccp4bb] AMORE_NSOL

Xue-Yuan Pei wrote: Dear ALL: I am runging AMORE and get an error message: AMORE: NSOL set too small When I checked the document, I could not find the keyword to reset NSOL. Any one can give a suggestion? Regards, xue This is a program parameter - it means you are working with more tha

Re: [ccp4bb] mr query

Can you combine the PHIC and FOM from each of your solutions, then do the Phase comparison in Clipper utilities checking for alternate origins? That gives a good indication of what is going on. Do you have more than one molecule in the asymm unit? You can finish up with A_phaser matching one

Re: [ccp4bb] refmac5 refinement with PEG400

You dont seem to have assigned LIBIN as 1pe.cif - you need to assign your library file - are you using the GUI? Enter 1pe.cif in LIB In slot. Craig McElroy wrote: Hi all, I am trying to refine a structure with a PEG400 molecule using refmac 5.3. I have created the necessary library file and

Re: [ccp4bb] mr query

The choice of origin is completely arbitrary as far as I can see - any or all of the alternates satisfies an MR search equally well.. Eleanor Kolstoe S.E. wrote: Thanks for the help everyone. I followed Jan's suggestion of running lsqkab which gave a translation vector in fractions of cell ed

Re: [ccp4bb] SAD: Refine against anomalous data

ping sun wrote: Thanks for your answer. I guess I did not make it clear. I used the data file for refinement which is also used for phasing (peak_anomalous.hkl). Traditionally, people will reprocess the same set of data for refinement (rescale it in hkl2000 without using the option "anomalous

Re: [ccp4bb] libcheck question

Whats in the cif file? Is it a set of coordinates or a library description? Eleanor Mark A Saper wrote: I'm new to using LIBCHECK. I'm trying to make an appropriate library for the MSO ligand. I have a .cif file that I downloaded from Gerard's site. When running LIBCHECK, if I use MON MSO and

Re: [ccp4bb] CCP4 rotation convention

I just have to write out matrices: CCP4 rotation matrix: [R11 R12 R13] [x] [R21 R22 R23] [y]where x y z are orthogonal coordinates relative to fixed axes... [R31 R32 R33] [z] represents a rotation of ccordinates by first gamma then beta then alpha as Phil says: [R11 R12 R13] [R21 R22

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

Ditto - I am getting everything in duplicate Eleanor Andy Purkiss-Trew wrote: Hi Ian and list, I don't know about rejected postings, as I've not made any recently, but I am getting two copies of each posting made and the second has gone through the same server as below: Received: from ms1.kiss

[ccp4bb] test 2

test 2

[ccp4bb] test

test..

Re: [ccp4bb] "Dry" structures

What does the matthews_coeff indicate? You would expect more water than that, but maybe you have a low Matthews_coeff indicating little solvent? maybe you have lost the low resolution data which makes it harder to find water? Maybe you have refined with bulk solvent scaling - sometimes that

Re: [ccp4bb] Structure help

Not enough information but some suggestions. Are you sure the data is OK? Any sign of twinning? That is suspicious if you cant decide between P43 and P43212 (Run SFCHECK on the amplitudes and try to understand output! ) Or send it and I will provide commentary. Eleanor Yanming Zhang wrote:

Re: [ccp4bb] The importance of USING our validation tools

rfactor? Quoting Eleanor Dodson <[EMAIL PROTECTED]>: The weighting in REFMAC is a function of SigmA ( plotted in log file). For this example it will be nearly 1 for all resolutions ranges so the weights are pretty constant. There is also a contribution from the "experimental" sigm

Re: [ccp4bb] Problem with VDW restraints in Refmac

Refmac will not introduce a repulsion unless the sum of the occupancies of the two neighbouring atoms id > 1.00 . Is that the case for you? ( It might list the close contacts - but shouldnt use them) If you want a link between the ligand and something else though you must label them both A or B

Re: [ccp4bb] The importance of USING our validation tools

://web.usc.es/~vanraaij/ <http://web.usc.es/%7Evanraaij/> On 16 Aug 2007, at 15:22, Randy J. Read wrote: On Aug 16 2007, Eleanor Dodson wrote: The weighting in REFMAC is a function of SigmA ( plotted in log file). For this example it will be nearly 1 for all resolutions ranges so the weights

Re: [ccp4bb] nature cb3 response - USING validation criteria

I am trying to keep track of, and notes on these Emails, many of which raise very important Qs for our community, much more so than any problems with a particulat structure.. But it would be a lot easier if you would all stick to the same Subject header!!! Eleanor

Re: [ccp4bb] High Rfac/Rfree for a 1.6A reso structure

There are obvious ones like - incomplete structure etc, but have you tried TLS? Sometimes this can dramaticaly improve the R factors. You seem to have lost of lot of the low resolution data - could this mean you had overloads which naybe could be rescued.. That can down grade the maps a good

Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

I think Garib or Alexei must answer this and they are both on holiday till the end of August Eleanor juergen J. Mueller wrote: Dear all, using refmac5 to provide H-atoms for a known protein structure the distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif. This distance has been

Re: [ccp4bb] [COOT] how to join the broken strand to the other whole molecular

I guess this is the old fashioned way, but it seems simpler to me! There are 2 strands labelled T I find it easier to run a program than use coot. distang xyzin 65*pdb RADI CA 3 end This shows you that A 85 -ish is linked to T 11-23 with symop X-1/2,-Y+3/2,-Z and B ??? is linked to T 41-53 wit

Re: [ccp4bb] solving structure of which 70% is known

Raja Dey wrote: Hello, I am trying to solve a multi-protein DNA complex structure from a 3.6 A native data set. The target structure is a dimer (95 aa in each monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. The data has been scaled to P6(1)22 sp. gr. and

Re: [ccp4bb] Rotation function calculation from 2 patterson maps

ALMN will do this .. It does not have a GUI - Gr #!/bin/csh -f # almn \ hklin /y/people/ccp4/projects/insmon/ins_p1_1,55A-I422cell.mtz \ hklin2 /y/people/jean/Youshang/monomeric/datproc/*mtz < Hi, I have two patterson maps created from two observed data sets of similar structures. I

Re: [ccp4bb] The importance of USING our validation tools

ZO has a good point - it is a pain trying to get decent simulated material - maybe there is an employment opportunity here? Eleanor Zbyszek Otwinowski wrote: James Holton wrote: How MUCH do you want to bet? ;) Any amount, as long as we are taking about real diffraction images correspondin

Re: [ccp4bb] contact density

Look at the MSDpisa page: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html reached from http://www.ebi.ac.uk/msd/ It probably tells you much of what you wantt o know.. Eleanor Mary Rorick wrote: Hi, I'm a evolution/genetics grad student trying to address protein questions. I'd like to f

Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622

If you have a high off origin peak at 0 0 0.5 you must have absences along the 00l axis also consistent with P63 22. So you need to test both P6322 and P6 22 And is the tetramer generated by crystal symmetry or is the whole thing in the asymmetric unit? Eleanor Jorge Iulek wrote: Dear all,

Re: [ccp4bb] Strange diffraction images

Beware twinning tests with pseudo translation! Intensity stats are distorted.. What does SFCHECK suggest? It pre-selects data for testing.. Eeanor Green, Todd wrote: I have a case that is similar to this, or at least visually similar by diffraction pattern(ie. strong/weak intensities). I thi

Re: [ccp4bb] Resid for occupancy

Vu Thai wrote: Hi, I have a protein that binds nucleotides, and in my structure, it appears that the binding pocket is partial occupied by ADP and AMP; the beta phosphate of ADP is transfered to another molecule. I want to refine the structure with both ADP and AMP modeled in the sight and manu

Re: [ccp4bb] Best program to find whether a crystal is twinned ?

Within CCP4 SFCHECK and TRUNCATE provide an analysis the PHENIX Xtriage is excellent.. See http://www.ccp4.ac.uk/dist/html/twinning.html Eleanor Jobichen Chacko wrote: Dear All, Can you please inform me the programs available to find whether a crystal is twinned and also the data reduction

Re: [ccp4bb] How many twinned crystals?

Not an expert on integration at all, but is this true for mosaic crystals when spots overlap rather messily? Eleanor George M. Sheldrick wrote: Since processing non-merohedrally twinned crystals became routine in small-molecule crystallography, the number of such twins has increased dramatical

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

You would have to edit the command script for PDBSET (From GUI - Run and View com file, then modify it..) There are options to select CHAIN A and protein only. etc etc Eleanor Antony Oliver wrote: You could simply hand-edit the PDB file to remove the offending ligand. Regards, Tony. H

Re: [ccp4bb] Why there is no C21 space group in crystal system

There are many alternate origins for different space groups.. However a somewhat arbitrary choice or origin was made for the first listing of independent space groups, and it is simplest to accept the established conventions. If you shift the C2 origin from 0 0 0 to 1/4, 0 0 you generate C21

Re: [ccp4bb] Covalently bound drug molecule

You need a LINK record in the PDB and a dictionary to describe the link. If you run the job from the GUI with Review Restraints, the program should write out a suitable dictionary to describe the link. Check the distances etc to see if you agree with them. You then use the extended pdb and tha

Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

No comment on the Auto debate, but the RMSD of bonds is a crude measure unless you check the outliers.. You can make REFMAC list these - I think it should do so by default actually.. Bad metal distances for instance can distort the number enormously. Eleanor Mark Mayer wrote: Hello all, I b

Re: [ccp4bb] HETATM to ATOM change, and atom identifier change in REFMAC...

That is very very peculiar! as far as I know REFMAC doesnt really care whether you call something ATOM or HETATM . I suspect the problem is either in the cif file describing the co-factor - could the atom type fpr MO be set as N? or possibly in the PDB file - is the Atom name displaced to the

Re: [ccp4bb] Another twinning question

First question - is the original PDB structure twinned? Can you download the data and check that.. And you have generated the extra models correctly have you - there are origin shifts to consider I think.. 2) How can you get an R factor of 20.7 / 25.7 with REFMAC in P6122 and one of 27.77/36

Re: [ccp4bb] model-mask

DM will produce its own mask if you provide the operators - the only time you really need a mask is for cross-crystal averaging. Eleanor m zhang wrote: Hi All, I was trying to make a model-mask file for ncs-averaging in DM. I noticed that in CNS, the mask file has to be O-compressed. Does

Re: [ccp4bb] Refmac5, .cif file for ligans and restrain.

I am not clear whether you want to apply NCS restraints to multiple copies of the same ligand type. That is easy - you just restrain Ligand CHAIN and "residue number1 residue number 1" in the same way as for protein chains ( Presumably residue number1 and residue number2 will be the same) If

Re: [ccp4bb] REFMAC and Hetroatoms

You need the atom name CA and CL moved one space to the left relative to C O N etc.. And correct the atom type in cols 76?? from C to CL and CA ( again moved one space to left) Eleanor Vineet Gaur wrote: Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refin

Re: [ccp4bb] anisotropic scaling in refmac versions

I cant answer - but this version certainly generates anisotropic scales.. We have ccp4.6.0.2 installed) ### ### ##

Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface

http://www.ebi.ac.uk/msd/ Go to msdpisa E Xiaoyi Deng wrote: Dear all: I used moleman2 to calculate the contacts between chain A and B. Can anyone suggest a program to calculate the contacts between the interface of dimer-dimer? Thank you, Xiaoyi Graduate student University of Nebraska

Re: [ccp4bb] refmac and ramachandran troubles

You havent got an incorrect CISPEP definition lurking in the PDB file have you - COOT does NOT correct these so if you rebuild something which has been previously flagges as CISPEP ( and that can happen if a very ugly omega angle falls to 89.999 ) then it stays that way in the PDB output from C

Re: [ccp4bb] calculating molecular dimensions

Well - PDBSET gives you the X Y and Z dimensions. ( pdbset xyzin thismol.pdb end If you want to align the protein along its principal axes, I usually run the TABLING function of Amore. That takes a model, moves its CofM to the origin and aligns it in such a way. Eleanor Vineet Gaur wrote

Re: [ccp4bb] Nearly perfect twinned data????

1) You dont say whether there is a non crystallographic translation vector - if that is so the twinning statistics can be misleading. SFCHECK analyses this or you can just run a native patterson to 4A say and see if there is an off-origin peak. 2) The twinning tests that use the correlation be

Re: [ccp4bb] FreeR flag value swap

You can just set your default FreeR value to 1. See the REFMAC gui etc.. Eleanor Petra Lukacik wrote: I have a mtz file (output from phenix AutoSol and AutoBuild) where the FreeR flag for the test set has a value of 1 and and the working set has value 0. This is opposite to the ccp4 default wh

Re: [ccp4bb] bfactor, freeR problems!!

Yes to keeping the same FreeR Bfactors - I doubt if it matters, but I usually start a new data set by setting Bs to the Wilson suggestion.. Twinned data - maybe you ought to use SHELXL to refine it? Eleanor john kryst wrote: Hi all !! I am working on some deletion mutants. Mutant

Re: [ccp4bb] Import and merge data collected from TWO sources?

There are two ways - 1) Import both sets - combine using CAD ( it is the first task of the Experimental phasing module) - do the automatic checking that you have the same indexing conventions - Scale data sets together ( 2nd task of Experimental phasing module) - that will give an R factor betw

Re: [ccp4bb] PDB Crazy or Me?

Did you go to this web site? http://remediation.wwpdb.org/downloads.html It has the new dictionary stuff Eleanor James Stroud wrote: Hello All, I noticed some things different about the PDB today causing me to rub my eyes vigorously and to put my nose right on my monitor in disbelief:

Re: [ccp4bb] atomic FF used in SFALL

I wrote that - is a constant a Gaussian? Anyway that is how I got 5 - and it is the 9-parameter Cromer-Mann approximation.. And Yes - each component is added to the B value to build up the real space atomic density. as you show. Eleanor Bernhard Rupp wrote: Dear All, I read in SFALL docu

Re: [ccp4bb] atomic FF used in SFALL

ented as series of Gaussians.a=0,b=0; a=1, b=0 This is called 'Gomputing'. Cheers, br -Original Message- From: Eleanor Dodson [mailto:[EMAIL PROTECTED] Sent: Thursday, October 11, 2007 1:26 AM To: [EMAIL PROTECTED] Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] atomic FF used

Re: [ccp4bb] Bad sidechain geometry

If the occupancy is 0.00 there will be no refinement - the output cds are the same as the input, and I guess that will make for horrible geometry - COOT will "correct" the geometry of all atoms though so you can make a prettier picture - but with no more information content re the model if the

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

These problems are horrible! 1) I usually try to run refinement using the exptl phases as restraints. It is worth getting the best possible phases before you start - DM with 66% solvent should make a great improvement.. Then these cam be used as restraints for the refinement, and your FWT m

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

You must be carefulwith assigning twinning operators in a lower symmetry than the true one. Some twinning tests look for correlations between reflections which would be related by the twinning operator. eg a twinning operator for PG 4 is k,h,-l so the CC between h,k,l, and k,h,-l is checked. B

Re: [ccp4bb] Electron density function for ligands in real space?

If you put the coordinates into COOT it will give you a validation score. If you use the CCP$i map correlation procedures it will also give you a CC for the density match. The input in each case is the reflection file with appropriate amplitude and phase terms. What you use depends on what p

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

Well - the wilson plots only indicate ice rings - they dont tell much about twinning, except that I would prob restrict the tests to exclude the suspect data. ( use resolution range low - to 3.5 for one, low - 2.4 for the other or some such..) The moments are the best indicators providing th

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

The cumulative intensity depends on correctly estimating weak reflections, so it is a bit vulnerable to the integration procedures. I prefer the 4th moment of E - 2nd moment of I. Providing there is no pseudo-translation they are pretty reliable indicators of twinning Eleanor Bryan W. Lepore

Re: [ccp4bb] converting structure factor files to mtz files

Use the CCP4i Reflection utilities Convert to MTZ and say you are importing mmCIF It will sort it out for you Eleanor Zheng Zhou wrote: Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to conver

Re: [ccp4bb] tricky molecular replacement

Yes- ALMN seems to have given one excellent match between the data sets which is encouraging. But since you are matching hexagonal to trigonal you get a large number of symmetry equivalent peaks, relating a molecule from the P1 set to one of the hexagonal set. The angles are defined so that: "T

Re: [ccp4bb] tricky molecular replacement

I would stop trying to use a map! that is an act of desperation when you have uninterpretable but possibly somewhat true experimentally phased density.. If you have a model it is MUCH MUCH easier! So as I said - I would find the best hexagonal dimer - you may know this or you can dispatch the s

Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 < 96) Phil On 8 Nov 2007, at 22:26, Brya

Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

te task would be an improvement. Phil Evans wrote: I agree On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list,

Re: [ccp4bb] SORTMTZ error status = 256

Can you attach the input file to sortmtz - the error is cryptic! I suspect the input file is corrupted somehow, but it needs testing. eleanor hari jayaram wrote: > Hi , > I have a low resolution dataset at 3.2 to 3.5 Å resolution , upon running > scala I get the following rather cryptic error >

Re: [ccp4bb] Pointless and space group P 4 3 2

Dont forget pointless gives a point group so you could have spacegroup P4123 too - check that in MR Could might well have a trimer sitting on the cubic 3-fold, but then the oligimer will be generated by the crystal symmetry, and you need only search with a monomer. Eleanor Kristof Van Hecke

Re: [ccp4bb] Problematic P2 dataset with pseudotranslation

These things are always very difficult. It is obvious from the TRUNCATE log that your data is incomplete past about 2.5A and that it is very anisotropic (See wilson graph and the anisotropy fall off graph.) ( but why do you say the data stops at 2.2 when the graphs go to 1.9A?) There doesnt se

Re: [ccp4bb] Poinless and space group P 4 3 2

Hurrah!!! I have quite often found that the packing requirements are too tight and ifell that they need at least to be given as a % of the CAs . MOLREP actually has a more sensitive packing check which looks at the % of the molecule which overlaps, and that is less likely to reject good soluti

Re: [ccp4bb] external phases in sharp

If you use the Clipper utiity HL to/from PHI/FOM it will generate HLA HLB HLC HLD of course HLC=HLD=0 but it serves to trick programs.. Eleanor Jan Abendroth wrote: Hi all, I am trying to include exteral phase information in a sharp refinement. The phases come from dmmulti. Steps this far: - c

Re: [ccp4bb] Summary: Symmetry of crystallographic stereographic projections?

A bit late but I didnt answer in time. This is one of the cases where I still wheel out ALMN to do the self rotation. It generates ALL symmetry peaks and allows you to select which axis you want to take as the polar axis. (ncode = 1 c*, ncode = 2 a*, ncode = 3 b* and so on) And the program out

Re: [ccp4bb] ncs phased refinement

Not enough information! Does the XYZIN file exist? Eleanor Raja Dey wrote: Hi All, I was trying to run NCS Phased refinement in the gui of CCP4 (Refmac_5.2.0005) and getting the following error. I just pasted below the last part of the log file. Any help is

Re: [ccp4bb] Occupancy refinement of substrate using refmac5

I dont think REFMAC can refine occupancy, but the way I would tackle it is to first refine B factors, then if those for the ligand are much higher than for the protein maybe test changing those occupancies to 0.7 , 0,5 and so on.. But in fact B factors and occupancies are highly correlated, an

Re: [ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file

You probably dont need to refine the positions but i guess there is no harm in it.. You do need to refine the ano occupancy which reflects the f" values. Your sites 2 and 4 are quite close so the MSE might be disordered? It doesnt really matter what you call the atom type since nothing is on th

Re: [ccp4bb] resolution & R-free

I doubt if you should ever t hrow away data if the I/SigI is sensible in the outer shell. Have you tried TLS refinement or loosened the B restraints? Often higher Rfree at higher resolution are related to B refinement problems. Eleanor 杨柳青 wrote: > Hi,dear all: > I try to refine one protein

Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

As you say - it is 17.006 in all versions of atomsf.lib I have access to! It is good that f' and f" will now reflect the wave length, although the wavelengh is so often wrongly recorded that this had better be an optional request rather than the default! Eleanor Ethan Merritt wrote: On Th

Re: [ccp4bb] How to refine large moleculars?

Yongchao Li wrote: I have a large molecule to refine.There are about three thousand residues in one asymmetric unit. Except for the lack of electron densities in several places, where the loops have been deleted, the rest parts fits well with density. But the R free and R work are all beyond 0.

Re: [ccp4bb] How to refine large moleculars?

With such good data you would expect lower R factors I agree. I use all the COOT validation tools - Ramachandran, diff map peaks etc to try to pinpoint errors. Also anomalous difference maps hoping to verify S positions and check the sequence fitting. You could let Arp/Warp rebuild it from t

Re: [ccp4bb] ideal bond length and bong angel

Bong angels are probably ideal already! There is really no such animal as an ideal bondlength or angle - they depend to some extent on the atomic environment. There are papers by Engh and Huber who looked at small molecule highly refined structures to get AVERAGE bond lengths and standard devi

Re: [ccp4bb] Sulfate ion on 2-fold axis

Jie Liu wrote: > Dear all > > I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file > one S atom with occu=0.5 and two O atoms with occu=1, or should > I put one S and four O atoms all with occu=0.5? > > Thanks for your inputs. > > Jie > > > It should be more or less equivalent

Re: [ccp4bb] ideal bond length and bong angel

Please do NOT use the BB for abuse. Eleanor Gerard DVD Kleywegt wrote: Be care, you insolence might get someone sent disappear. is the chinese secret service editing my incoming mail already, or are you merely using a microsoft grammar checker? --dvd *

Re: [ccp4bb] scale data with multiple MTZ files

The task - Sort/ Modify / Combine files does just that.. Eleanor Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3

Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?

It needs Garib to answer this! Eleanor Charlie Bond wrote: > Eleanor Dodson wrote: > >> It should be more or less equivalent, but better I think to put 1S at >> 0.5 occ and 2O at occ = 1 >> >> At least in REFMAC the restraints to the symmetry atoms should be se

Re: [ccp4bb] wich program to test an alternative phaser solution

PDBSET xyzin model.pdb ROTA EULER a b c SHIFT FRAC tx ty tz CELL new cell end Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution.

Re: [ccp4bb] Calculating volume of Ligands

It isnt a bad approximation for any organic compound to take the number of atoms including hydrogens, and multiply it by 10A^^3 Eleanor Dodson Rajan Pillai wrote: Hi All, Can anyone tell me any program that calculates voume of a ligand? Moreover, is there also any program that can calculate

Re: [ccp4bb] difference between I over sigma_I and I over sd

LLI agree the difference between sd and SigI are a bit obscure. One referes to the spread of values about your mean I (The Sd of the reflection distribution) SigI is derived from the SIGI values estimated by the integration. There is some description in the CCP4 study weekend article by Phil Evans

Re: [ccp4bb] Spacegroup choices, reindexing and so on

These decisions are always going to be individual but I have been pushing for a long time for the mtz output to have a pointgroup at the data processing/merging stage with a check list of spacegroups in the order of their probabilities ( as pointless now suggests..) . There could then be a seper

Re: [ccp4bb] Help Superposition programmes!

Yes - you are right! It doesnt work on my PC either.. I dont understand the code at all. Did it work on an older version of CCP4? Eleanor Anita Bentley wrote: Dear CCP4-programmers, I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - u

Re: [ccp4bb] Why there are difference density when occupancy is 1.00

Hard to say without more information. Have you refined the B factors for these residues? Most building software gives some arbitrary b value, which must then be refined. (In fact after any rebuilding activity you need to do a few cycles of refinement before looking at the maps again) Eleanor

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