Re: [ccp4bb] monomer library in refmac5

Hmm - I think this is a bug.. Garib - what do you think? Eleanor Jianghai Zhu wrote: Dear all, I have some N-acetyl-glucosamine (NAG) in my structure. When I searched the monomer library in CCP4 6.0.1, I found out that NAG is actually N-acetyl-glucose, which is much less common, I believe.

Re: [ccp4bb] Problems in MR

You dont say the spacegroup. Different MR solutions can exist relative to any of the acceptable alternate origins. Eg If it were P21 say the two solutions could lie anywhere along the b axis. Try running superpose (coordinate utility ) matching sequences. If the rotation looks like a symmetry

Re: [ccp4bb] MTZ to Shel-X?

That is done I believe in mtz2various.. Eleanor George M. Sheldrick wrote: I would like to second Ian's bug report, and suggest one minor improvement. Rather than multiplying I and sigI by 10, one could find the largest intensity value I(max) and multiply all the I and sigI values by (say)

Re: [ccp4bb] : MTZ to SHELX question

Assign LABI I(+)= etc I(-) etc OUTP SHELX and I think you get what you want.. Eleanor Nat Echols wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** A coworker recently solved a structure at high

Re: [ccp4bb] MTZ format conversion

This is possible but a bit of a pain.. - you need to make an mtz file, convert it to the multi record format, go through a scala step to reformat that then you get back to the mtz with h k l Fmean Dano F+ F- Imean I+ I- all on one line.. I have such a script but it is not part of the

Re: [ccp4bb] practical limits of MR?

Congratulations - That is amazing - did you find both molecules even though they differ? Eleanor William Scott wrote: shameless-plugWe just solved a 142 nucleotide asymmetric unit of a novel ribozyme structure using only A-form RNA helical fragments and phaser. I'm trying to find some time to

Re: [ccp4bb] MTZ format conversion

How do you solve the anomalous data Q - this might be useful for SHELX too - the reflections do not have to follow each other, or I believe even by hkl and -h -k -l; they can be a symmetry equivalent.. E Kevin Cowtan wrote: Here's an updated version of cns2mtz. The new version automatically

Re: [ccp4bb] Sketcher and stereochemistry

Whatever you do it is good practice to do your first run of refinement as Review Restraints Under the Monitoring folder set the level to many (default medium) and set the sigma cut off for chirals to 3.00 say to get a god list Then run the job and you will get a list of violations of restraints

Re: [ccp4bb] ccp4 pdb format

yang li wrote: Hi: Now I need to input a heavy atom pdb file in the ccp4 interface, does ccp4 has a special format for all the programs in the package? I used heavy atom file from shelxd but it seemed not right. where can I get a model of such pdb file? Thanks! SHELX has its own

Re: [ccp4bb] Generate Random phase set.

You can do that to some extent by scattering random atoms about and calculating phases from them.. Then the centrics will be sensible. That is how some direct methods programs get their random starting set of phases.. Depends on how flat you want the starting map to be Eleanor David Briggs

Re: [ccp4bb] modelling with sad/mad data

You dont say the size of the protein but in fact errors in f' or f will have very little effect. You can correct the SE formator if you like, but even so in most cases if you call the MET MSE then you get holes over the Se in difference maps which probably indicate partial conversion. Frankly any

Re: [ccp4bb] antibumping restraint in Refmac

Well - it happens by default. Do not wantt to tighten the restraint? Eleanor Kristof Van Hecke wrote: Dear, I was wondering what is the best method for applying 'anti-bumping' restraints in Refmac? (e.g. for preventing some specific water molecules coming too close to each other) Many

Re: [ccp4bb] Highest shell standards

This is a good point - I had thought that D would be very low for an incomplete shell, but that doesnt seem to be true.. Garib - what do you think? Eleanor Petrus H Zwart wrote: I typically process my data to a maximum I/sig near 1, and completeness in the highest resolution shell to 50% or

Re: [ccp4bb] How to subtract one electron density map from another

Qing Xie wrote: Hi, I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? Thanks in advance, Qing

Re: [ccp4bb] Merohedral twinning

1) Why do you think there is twinning? If you label a structure whose true spacegroup is H32 as having SG H3, then some of the twinning analyses report that this is consistent with perfect twinning.. I believe the graphs of the moments from TRUNCATE give a true indicator. Ditto the latest

Re: [ccp4bb] Right Handedness of Density

You dont say how you solved this, but usually now the solution methods should give the correct hand, providing you indexed the data correctly and did not muddle up hkl and -h,-k,-l measurements! Fromm the heavy atom search you cant tell the hand so both x,y,z in P32 and -x,-y,-z in P31 will

Re: [ccp4bb] Strange Density

Superb picture - thankyou - will add it to the lab gallery! Eleanor William Scott wrote: Hey, dude, thanks for writing! I could swear (so to speak) You sat next to me on an 11 hour airplane flight not too long ago and tried to strike up a similar conversation. I apologize for being too

Re: [ccp4bb] Unusual Difference Fourier near Methionines

I think the SD-CE is pointing the wrong way. And they look much too close. I would rotate them and re-refine Eleanor PS - any noise on the 3 fold axis will be multiplied by a factor of 3 Ethayathulla Abdulsamath wrote: Dear all I am doing one structure at 2.6A resolution where I found

Re: [ccp4bb] Differentiating bound Mn Ca.

In cases like this I use the S atoms to calibrate the peak height. Of course it isnt definitive a) it is near the noise level, and b) peak height is very dependent on B factor.. But the ratio might distinguish between an atom with an f of 1.3 or f=2.8 Eleanor David Briggs wrote: Dear all. I

Re: [ccp4bb] Rfree continues to decrease while Rcrys is more or less static

This is unlikely to be the result of the method you used to solve the structure. It is probably due to you having some NCS related reflections in the free set and some not. First consider the direction of your 4 fold - could you have a higher symmetry space group? Eleanor Vineet Gaur wrote:

Re: [ccp4bb] weird thing about MR

Such high R values usually mean there are many many very weak relections.. You havent kept in the h+k+l = 2n+1 reflections have you? Do a native Patterson check too to make sure there are not other translations which might distort the data Eleanor Yi Xue wrote: Dear all: I have a

Re: [ccp4bb] NCS-averaged composite omit map?

Use COOT to do NCS averaging then look at the maps of B onto A a well as the averaged one to see where differences might be. Eleanor Paul Paukstelis wrote: I'm working on a 4.5-A structure with 4-fold NCS. I've generated a SA composite omit map and all the protomers look pretty good, but with

Re: [ccp4bb] weird thing about MR

You say you have only found one of at least 3 copies? Why not continue and find the other 2 before starting refinement? Phaser will do that automatically if you ask for 3 molecules.. Refinement of structural fragments is always tricky.. Eleanor Yi Xue wrote: Dear all: I have a dataset

Re: [ccp4bb] extra high B factor

Well - it is extremely likely that the peptide is partially occupied and the occupancy may well be 0.5.. But at this resolution you are going to have great difficulty deciding whether you should have Occ=1.0 B = 130 Occ = 0.5 B = 100 Occ = 0.33 B = ??? 80??? As your Rfactors show it

Re: [ccp4bb] mlphare ref

I believe if you go to the CCP4 main page you can find: http://www.ccp4.ac.uk/courses/procs.html 1991) Isomorphous replacement and anomalous scattering. DL/SCI/R32. Contents Available. http://www.ccp4.ac.uk/courses/pastprocs/dl_sci_r32.html Eleanor Bernhard Rupp wrote: Dear All, I failed

Re: [ccp4bb] Refining alternate ligand/autoinhibition

Well - A and B are meant to be flags to show there are 2 conformations of a particular unit. sp they arent appropriate here and may be muddling things up. On the other hand you shouldnt get any repulsion between pairs of atoms whose added occupancy is = to 1.0 Is that always the case for

Re: [ccp4bb] How can I refine Mg2+ with REFMAC?5.2

Dirk Kostrewa wrote: Dear CCP4ers, I try to refine a protein structure with a Mg2+ bound. In the REFMAC5.2 dictionary, I only found a neutral Mg and several (strange) entries of different water-coordinated Mg2+ with some predefined water naming that I don't want to use. I would just like to

Re: [ccp4bb] references for TLS refinement

Nalam, Madhavi wrote: Hello: I am planning to cite the following references (which are given in the CCP4 program references) for TLS refinement. * B.Howlin, S.A.Butler, D.S.Moss, G.W.Harris and H.P.C.Driessen, TLSANL: TLS parameter analysis program for segmented

Re: [ccp4bb] Program to find the center of mass

MOLECULE: 27.449 -14.779 52.855 CENTROID OF REFERENCE MOLECULE:(fractional)0.165 -0.149 0.324 Distance between CENTROIDS : 181.751 Direction cosines of vector between CENTROIDS: -0.634 0.721 -0.281 Eleanor Dodson Nian Huang wrote: Dear all

Re: [ccp4bb] rmsd calculation

It is a bit clunky - you can use siperpose molecules - fit residues to fit a selected range (1-40; 60-100 say) and write out a complete fitted pdb file. Then you could use a VERY old program compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb) and it will match all pairs with the

Re: [ccp4bb] xsect.dat=cossec.lib?

Bernhard Rupp wrote: Dear Coders, Do I see this correctly that crossec.lib is the XSECT.DAT file from Don Cromer's FPRIME program? If so, has there ever been an update? Mine is from some reel tape I got from him long ago when I ported the code...seems to be the same. Thx, br

Re: [ccp4bb] Mol Rep in high symmetry spacegroups

High symmetry for me means F432 .. no particular problem in H32 And of course the more molecules to find in the asymmetric unit the more difficult it is.. But the general rule is Rotation function harder the higher the symmetry - more likely to have overlap between crystal symmetry and NCS

Re: [ccp4bb] Disordered active sites

Nian Huang wrote: Hi, all, I met some crystal structures with disordered active sites. Soaking common ligands can not make it become ordered. I am wondering what people generally do in such situation. Thanks, Nian Huang Swear?! This is quite common - the usual tricks may work - Sulphate ,

Re: [ccp4bb] crystal problems

Detwinning without a known structure, and such a high twin factor must be very unreliable . If you have only IT1 and IT2, the detwin algorithm gives I1 = (TF*It1 + (1-TF)*IT2) / (1-2*TF) (Maybe signs wrong there!) Since (1-2*TF) is almost 0, this is pretty inaccurate.. But if you

Re: [ccp4bb] scala and cell dimensions

I dont know but I would check whether there is some residual P422 info somewhere.. Eleanor Jan Abendroth wrote: Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however

Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

There are several scenarios and it is hard to generalise. Certainties are: 1) The better your data the easier it is to see a ligand. At 3A it can be hard to model a blob, but it is usually straightforward at 2A. It is harder if your data is twinned etc.. 2) There is a lot of unnecessary and

Re: [ccp4bb] Rfree into an existing mtz...

uniqueify this.mtz this generates all indices to your high resln limit, adds freer and outputs this-unique.mtz Is this what you want? Eleanor James Pauff wrote: Good day all, What is the best means of getting a freeR column into an existing mtz file? I've noticed the Edit MTZ command bar

Re: [ccp4bb] refmac crashes when ncs restraints are applied

I certainly have used NCS restraints with ccp4-6.0.2 That doesnt help much though does it! Eleanor [EMAIL PROTECTED] wrote: Date: Thu, 31 May 2007 14:57:03 +0100 From: Stephen Brian Carr [EMAIL PROTECTED] To: ccp4bb@jiscmail.ac.uk Subject: refmac crashes when ncs restraints are applied

Re: [ccp4bb] B-factor Space gr questions!

Yes; a==b for P6i - prob. a typo.. B factors at 3.2A are hard to fix - it will depend on scaling convention to some extent.. Can you download the data and re-run refinement for your own satisfaction. If R ==Rfree for the complex then I suspect they did not transfer the FreeR flags from the

Re: [ccp4bb] refmac fails on iodine ions

Two things I think 1) I is a metal so you need to move the atom name 1 space to the left - more like this: ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 I I B 1 19.956 22.770 18.597 1.00 30.00 I And the monomer library

Re: [ccp4bb] DANO from PDB

Santosh Panjikar wrote: Hi all, Does anybody have a program which can calculate anomalous differences or F+ and F- from a refined structure at given wavelength and resolution ? Thanks Santosh Santosh Panjikar, Ph.D. [EMAIL PROTECTED] Staff Scientist EMBL Hamburg outstation

Re: [ccp4bb] b-factors from refmac tls refinement vs cns mlf refinement

These are B factors RELATIVE to your TLS parameters. You need to run tlsanl to get back to something comparable to the individual B factors.. Eleanor CRAIG MCELROY wrote: Hi all, I'm working on the structure of a heterodimer phased by molecular replacement using data to 2.9 angstroms. After

Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

I suspect you can use the Reflection utilities Convert to mtz and ask for mmCIF input - this is meant to be mmCIF compliant.. I think? Eleanor U Sam wrote: Hi I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file created in shelex. I can load .fcf file in coot to see the

Re: [ccp4bb] B-factor sharpening in CCP4 or Coot

There is a CAD option to apply a scale and B factor to any set of data, and an FFT option to apply a scale and B factor to any column in the map. Check the documentation for whether you need SCALE 1 -10.0 or SCALE 1 +10.0 ! Eleanor Jeff Lee wrote: Hi, I have a question for everyone. I

Re: [ccp4bb] bond length constraints in refmac

Craig McElroy wrote: Hi all, I'm refining a structure in refmac and for some reason it does not seem to constrain bond lengths so when I look at the structure after refinement many of the bonds are broken (i.e. too long). I know that you can add distance restraints in the geometric restraint

Re: [ccp4bb] Fw: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

Is COOT complaining because the SHELX output PDB has no spacegroup? If you run pdbset xyzin shelx.pdb xyzout shelx1.pdb SPAC P21 ( say) end it will add the SG to the CRYST1 card Eleanor Eleanor Paul Emsley wrote: Thanks George, Yes, COOT can open fcf.file and make beautiful maps. But I

Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

Coot has an expert mode which allows you to customise your FFT to some extent - you will need to turn the fcf file into an mtz file, but that is easy.. ( See reflection utilities) And then you can use the great flexibility of the FFT routines to generate a map to read into COOT. Eleanor

Re: [ccp4bb] SFALL problem - weird atom maps

I understand this surprising feature now .. The atomic density is being smeared by the BADD 100 to cover a volume 3A from the atomic centre. (3.2A to be more precise..) But the limit on the map sections to be included in the inverse fft is calculated without that BADD - in fact you use the

Re: [ccp4bb] space group R3(R32) or H3(H32)?

There is a lot of confusion about this! You can call it R3:H ( indexed with a=b and gamma = 120) This is also called H 3 in the PDB deposition and the CCP4 symmetry libraries. (But for the CCP4 library - it checks the axes and angles to decide whether this is using the H ( or hexagonal)

Re: [ccp4bb] how to convert matrix to angle

This sort of information is summarised on the MSDpisa site http://www.ebi.ac.uk/msd/ Eleanor U Sam wrote: In this connection I like to know how symmetry (in degrees and translation) is calculated between two or more molecules in the asymmetric unit (A.U.). Suppose if I download a PDB then

Re: [ccp4bb] twin

Look at http://www.ccp4.ac.uk/dist/html/twinning.html for introduction.. Eleanor Li Sheng wrote: Hi, Dear All, How could I know whether a crystal was twin or not from it's diffraction data? Thanx in advance. Sincerely, Li 07-08-2007

Re: [ccp4bb] shelx HKLF4 to mtz conversion?

Is this a SHELX data set where the FreeR is flagged as -1? There seems to be a variety of methods .. But if you read in the FreeR flag from SHELX and ask to have a FreeRflag output the convert -t o - mtz script under Reflection data utilities will output the SHELX value Eleanor Leonard

Re: [ccp4bb] Metal-ligand(s) positioning following refinement...

Yes there is a way to do something anyway. Is your metal only linked to protein or are there extra atoms as part of the metal? If there is protein lins you need to make a LINK record in your PDB and provide a dictionary description of your expected geometry. If you have more details I can

Re: [ccp4bb] modelling radiation damage of Asp/Glu (occ vs. B factor)

John Pak wrote: Hi all, I was hoping to receive some guidance on the following subject. I'm refining a structure using REFMAC that shows all the symptoms of radiation damage. Namely partially broken disulphide bonds and decarboxylated Asp/Glu residues. I have an idea of how to handle the

Re: [ccp4bb] Twinning in C2 ?

You dont say whether the molecules in the native cell form a dimer - if so I would search with that (you may need to turn off the packing search) Or whether there is a pseudo translation vector in the mutant form.. Or what the data analysis graphs from TRUNCATE show - are they normal? Eleanor

Re: [ccp4bb] Twinning in C2 ?

are getting from molrep ? many thanks Demetres P.S. I will summarize for the members of the list all the suggestions I will get at the end Eleanor Dodson wrote: You dont say whether the molecules in the native cell form a dimer - if so I would search with that (you may need to turn off

Re: [ccp4bb] extend resolution in refmac

Do you mean you only have experimental data to 2.3A - if that is the case I am afraid you cant force REFMAC to work to higher resolution. Do you mean you just want SFS calculated to 2.2A ? Eleanor JOE CRYSTAL wrote: Dear all, I am refining a structure in Refmac at 2.3 A and I set

Re: [ccp4bb] calculate B-factor of individual parts

baverage xyzin prot.pdb end Will give you something of what you want.. Eleanor fang sheng wrote: Dear all, The refmac output lists B-factor of each individual atom. But how can I get the B-factor of each set of group, say, protein, ligand A, B, and all 300 waters? suzi

Re: [ccp4bb] Combining MR and MAD phases

1) Combine your MAD 3A phases with the 1.7A native data and use DM or Pirate to refine and extend the phase set. 2) Make sure your MR solution is on the same origin as the MAD phases. You can calculate PHIC and FOM from MR solution, combinre with the MAD phases and do an anomalous diference

Re: [ccp4bb] need help--Rfree is not decreasing

First suggestion - use WEIGHT AUTO in REFMAC - you may have restrained the geometry too tightly.. And have you tried TLS ? And at what level do you see no density - remember sigma levels in maps need to vary with B factor - very easy to achieve this with COOT.. Eleanor JOE CRYSTAL wrote:

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

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 F v Fcalc as a function of resolution? If so you probably need to use SCALE SIMPLE - in gfact that is

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

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

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

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

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

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

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

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

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 greatly

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

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

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

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

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

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

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

[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

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

and 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 sigma, which in this case

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

/%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 are pretty constant. There is also

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

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] 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 eof CROSS 15 resol 10 3 CRYSTAL FILE 1 ORTH 1 LABIN FILE 1 F=F_P1 SIGF=SIGF_P1 CRYSTAL FILE 2

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

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

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

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

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] 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

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

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

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

<    1   2   3   4   5   6   7   8   9   10   >