Re: [ccp4bb] Very weird

It seems very odd..in fact almost impossible. You still have 3 correct molecules I wonder if there is some error in the coordinate file? Errors I make are: leaving and end record, between 2 parts. - many programs stop reading coordinates at the first END leaving CRYST1 and SCALE cards in t

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 o

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) 99

Re: [ccp4bb] MTZ format conversion

All formats I know except CNS have single records per reflection. In CNS a reflection record can go over several lines - I know no way of avoiding requiring a format tt to read such a record.. A clever programmer could parse a few lines and work one out, but in fact the format is not nec. co

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 resolution

Re: [ccp4bb] : MTZ to SHELX question

Truncate does not change intensities, only amplitudes. (Why should it? ) Eleanor The mtzvarious output will have what you want.. h k l I+ -h -k -l I- Nat Echols wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk

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 Refle

Re: [ccp4bb] practical limits of MR?

Congratulations - That is amazing - did you find both molecules even though they differ? Eleanor William Scott wrote: We 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 write the paper

Re: [ccp4bb] XDS to MTZ for SOLVE

But SOLVE will read an mtz file? I dont think you need to do this.. Eleanor Santarsiero, Bernard D. wrote: Not purely a ccp4 question, but an MTZ file is involved, so stick with me. I've collected a SAD data set, and processed with XDS. I can use XDSCONV to generate an MTZ, SHELX, and CNS file

Re: [ccp4bb] Protein PDB in Crystal Environment

Well - you kind of need to be selective I find. Here is a totally unautomated procedure! I run DISTANG (DIST INTER RADI CA 3) or NCONT to find all the sym ops which give contacts between molecules, then use PDBSET to generate those sym ops I like pdbset xyzin 1.pdb xyzout Si.pdb symgen 2-x,y-

Re: [ccp4bb] High overall b-factor

There have been other discussions of this. In fact if the data peters out at 3.2A I think you would expect such a high B. But also it is quite difficult to estimate the overall B for such a data set - look at the Wilson plot from the Importscaled data step and see what value it suggests? Elea

Re: [ccp4bb] Differences in R and Rfree

Yes - your real problem is probably that the Rfac is too low and that is often due to have rather loose geometry or lots of unrealistic waters in the model (RmsD on bonds of > 0.03 say..) It is all a bit unrealistic if you say your maps are good. I suspect if you tighten the geometry restraint

Re: [ccp4bb] modelling with sad/mad data

First it is always best to refine your model against the highest resolution good quality data that you have available. There was correspondence about the geometric weighting - could you have weighted the Xray data too high and have bad geometry - see previous Emails! And the Free R seems rather lo

Re: [ccp4bb] RMSD

Well - it reflects agreement with the dictionary - I guess there may be differences. Certainly there was at least one error - in THR CB-OG1 I think .. And others may have been corrected.. Eleanor john kryst wrote: Hi ccp4bb !!! Does the rmsd estimation (for eg. rmsd_bonds ) depends on the pr

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 m

Re: [ccp4bb] refmac refinement and multiple conformations

Rfactors are ALWAYS different from those quoted I think! They depend very much on the scale factor estimation, and that differs from program to program (and version to version) Eleanor REFMAC certainly can handle multiple conformations.. yang li wrote: If a pdb file contains some residues

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 interpretati

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 thank

Re: [ccp4bb] Highest shell standards

I feel that is rather severe for ML refinement - sometimes for instance it helps to use all the data from the images, integrating right into the corners, thus getting a very incomplete set for the highest resolution shell. But for exptl phasing it does not help to have many many weak reflectio

Re: [ccp4bb] Scale factor in ccp4

When youu run scalepack2mtz the GUI always follows this by TRUNCATE to convert Is to Fs At that stage there is an attempt to put the data on roughly an absolute scale, either using the NRES you gave as input or if that is not set, I think assuming 50% of the cell volume is protein. Anyway the

Re: [ccp4bb] Scale factor in ccp4

write out the combined .sca file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 22 Mar 2007, Eleanor Dodson wrote: When youu run scalepack2mt

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 Ye

Re: [ccp4bb] Solving a structure by MR with a pseudo-translation vector

These structures are horrible.. Remember you do not know your spacegroup. Absences along 0k0 and 00l will be very influenced by the translation. Sp you need to test all: P21 2 2 P21 21 2P21 2 21 P21 21 21 Run MOLREP using the pseudo translation vector - it is an option in the GUI under

Re: [ccp4bb] Highest shell standards

What resolution do you have? I have always been a bit sceptical about this, since if nothing is measured because of the anisotropy no sharpening will generate a term .. The "free lunch" algorithm is certainly useful. We used this with ACORN to correct phases at high resolution, setting all m

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 SFCH

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 gi

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 engrosse

[ccp4bb] ECM24 Morocco

Message from Eleanor Dodson I am chairing a session at the ECM 24 to be held in Morocco at the end of August on *Advances in crystallographic phasing and refinement* I am interpreting this as mostly to be about Macromoolecular studies. There are 6 slots for speakers

Re: [ccp4bb] antibody refinement in REFMAC with Kabat numbering

John Pak wrote: Hi all. I'm currently refining an Fab structure. All was going reasonably well until I renumbered the PDB according to the Kabat numbering convention. After which, REFMAC does not refine the inserted residues properly (ie. residues 82A, 82B, 100A, 100B, 100C, etc.). It refi

Re: [ccp4bb] Post facto fix to R-free selection

Probably easiest to start again with the correct FreeR You can perturnb the strucures pdbset xyzin MR.pdb xyzout- MRshaken.pdb NOISE 0.3 That moves everything a bit. Or if you do enough cyles the FreeR should increase steadily to a sensible value then level off Easiest to use the GUI and cl

Re: [ccp4bb] SAD question

John Bruning wrote: Hi, I have some questions regarding SAD. Can one use Scaleit to initially analyze anomolous data when doing SAD (ie to get the scaleit.summary statistics)? How does one properly prepare the flags and mtz file for SAD (ie what program to convert the sca file to mtz and p

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 unu

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.

Re: [ccp4bb] twin fraction varies between crystals?

This is a very common thing - twinning is a sort of accidental overlap of crystal fragments and thus will be different for diferent "crystals". ( Should a twinned object be called a crystal? Discuss) More serious - it is probably different for different parts of the data collection if your cr

Re: [ccp4bb] twin fraction varies between crystals?

This is not definitive, but in a similar case - P21 with a~c, we could detect twinning from the moment plot in TRUNCATE with 15% of data.. (ie run SCALA and TRUNCATE option - scales poorly determined, and I think we fixed them to unity..) Eleanor That meant you could test the crystals at ho

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] MAD and twinning

Well - it is pretty tricky to get reliable anomalous signal after detwinning, but I guess you can try! There are 2 ways I would test - one is detwin assigning I+ and I- - it is meant to handle the anom pairs correctly.. You can input the twin operator and the twin factor. Then SFCHECK will

Re: [ccp4bb] R and Rfree

It is difficult at the end of refinement - the small corrections hardly affect the R values, but should make the maps look cleaner. And R values are very correlated with the tightness of your geometric restraints - maybe you are changing these slightly too? I presume you are describing small sh

Re: [ccp4bb] Superposition of maps from different crystal forms

Well - I would do it the same way as you are - find a matrix with lsqkab, then apply that to the map with maprot. It should be OK. However there are some tricks which might help. Small differences in cell dimensions sometimes muddle coot I think and also I think it gets confused by different s

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 datas

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] buried surface area

I use PISA - it tells you lots of things and I think will do this as well http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html You can download your coordinates.. Will need to name subunits A and B or something I think.. Eleanor Gloria Borgstahl wrote: Hello all, What is the easiest way, th

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 d

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 Occ = 0.5 Occ = 0.33 As your Rfactors show it makes very little difference t

Re: [ccp4bb] can truncate import Rfree?

Are you using the GUI - one of the options in the Data Reduction menu under Import merged data is to copy Rfree from another mtz file.. TRUNCATE doesnt actually do it - the script runs TRUNCARE then CAD then freerflag to complete the assignment for any missed reflections.. Eleanor Tim Grune

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. Eleanor Bernhard Rupp wrote: Dear All, I faile

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 yo

Re: [ccp4bb] difficulties to determine the space group

complicated. Leaving aside the screwyness presumably it processed as PG422 OK. Checks 1) NCS translation? 2) Twinned?( both can be checked with SFCHECK - it will tell you if there is pseudo translation and make a guess at whether there is twinning.. The log file is terse but should giv

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 r

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 anisotro

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

.010 CENTROID OF "REFERENCE" 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 -

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] Molecular Replacement issues with a WD-40 7-bladed beta propeller

You dont say how close your sequence ID is for your new protein and the model. It is often very hard to kick start refinement with low homology And what about internal symmetry Is there a Non crystallographic translation? Does the self rotation function show a relationship between the two mole

[ccp4bb]

I presume you tried P32 21 also? Pointless cannot distinguish the difference.. Refinement at 3A is tricky - you can overfit quite easily and maybe Rfree is correctly flagging that there are still errors. Can you see features which need rebuilding? Eleanor Emmanuel Prata wrote: Dear all, I

Re: [ccp4bb] Low resolution model building

I have used many methods to do this over the years, but now I would never consider using anything but the COOT interface. The NCS operators that COOT uses are based on the SSM (secondary structure matching) program written by Eugene Krissenel. You read in your coordinates into coot and it re

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 Tr

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

Jay Thompson wrote: Hi, I have a question with molecular replacement using Phaser. I'm trying to solve a complex and I have a partial molecular replacement solution solved using another program. This solution is correct and makes up ~50% of the entire complex. I wanted to fix this solution

Re: [ccp4bb] Refmac5 restrained refinement could not keep the changes made in Turbo

Have you adjusted the wighting scheme from 2A - you want to relax the geometric restraints at 1.2A - best to use WEIGHT AUTO.. Eleanor XJ XJ wrote: Dear all, I am having a problem with refining my structure using refmac5. Basically, I am trying to make some small changes to several places on

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 have

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 dies

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 co

[ccp4bb] Improving the GUI

on June 11th and 12th. Once that is done we will call for suggestions for the second more challenging stage. the third stage will probably be part of the next CCP4 grant application. As a preliminary to Stage 1, can you Email Eleanor Dodson with your gripes ([EMAIL PROTECTED]) An example

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 Message

Re: [ccp4bb] Second moments of Z but not twinning

Have you looked at http://www.ccp4.ac.uk/dist/html/pxmaths/index.html It is an introduction .. Eleanor Randy talked about deviations at the CCP4 study weekend this year.. Winter, G (Graeme) wrote: Hi Folks, I was wondering if there is a document somewhere explaining some of the more intere

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 a

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 cal

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] DANO from PDB

Well - the old way to estimate sigma was Sqrt(I**2 + constant_representing background) and then get Sigma_F as ~ sqrt(SigI)/(2*F ) . sftools would calculate that for you and append it to the output file.. Eleanor Eleanor Peter Adrian Meyer wrote: I add a fake "sigma" column for each "data" col

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 ma

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 want

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 s

Re: [ccp4bb] CCP4 - Monomer library sketecher

Sridhar Prasad wrote: I would like to know if the following options exist in the monomer library sketcher: 1. To assign a specific residue number and chain ID to the ligand/inhibitor. 2. To have the PDB file (*_libcheck.pdb) written out such that all the H atoms coordinates are after the heavy

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 d

Re: [ccp4bb] questions about hydrophobic core

I dont know the answer but have you looked at the PISA site at the eBI - there is extensive documentation addressing these sorts of questions. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Eleanor Sebastiano Pasqualato wrote: Hi all, a few days ago I sent a post in which I was asking if an

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] number of MTZ files input to scaleit

No - I guess CAD should be updated but it is slow .. E Harry Powell wrote: Hi folks silly question, I know, and I'm sure this must have been answered before, but I want to put 10+ datasets into the same file and get scaling statistics between them. I find that SCALEIT is happy to do the sca

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) convent

Re: [ccp4bb] how to convert matrix to angle

Coot (and SSM) should give matrix - euler and polar angles! Paul? Eugene? But if you do the superposition with lsqkab (superpose molecules - match residues) then that gives all 3 ways. Or use ROTMAT which converts everything to everything else.. ( rather clumsy though..) Eleanor Jiamu D

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 I

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] protein contacts

msd pisa does that eleanor [EMAIL PROTECTED] wrote: Dear all, I’m wondering anyone can recommend some programs or servers to evaluate protein-protein contacts. I’m currently have a homogeneous tetramer. However, the protein exists as a dimer in solution. I’m thinking where to cut the line

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 Tho

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 b

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 pa

Re: [ccp4bb] Asking help about refmac5?

Some answers: Re FreeR increasing? 1) Have you been careful to keep the same FreeR set for the REFMAC and CNS refinements? I suspect not and that explains why your first FreeR is unrealistically low, and then increases to a more realistic value. If you use the GUI and select "Create mtz file" from

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"? Eleano

Re: [ccp4bb] Twinning in C2 ?

tion to the solution we 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

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 resolution

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 map,

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:

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