[ccp4bb] fix or scale bfactors during processing?

Hi all I have pretty low res data (4-4.5A) and was wondering what's the suggestion for allowing the bfactors to vary or keep them fixed during scaling. If I fix them, xtriage reports wonderful anomalous signal whereas if they are varied, the anomalous signal is gone. I have natives and su

[ccp4bb] Using own orientation matrix with imosflm.

Hi All I have a predetermined matrix from labelit, how can I use it with imosflm? I add the matrix file under 'Images', but I cannot integrate. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu

[ccp4bb] multiple datasets in Xds

Hi all Can XDS take in additional images that have a different template name and reside in a different directory? The reason is that I have high res images and then low res images in different directories that I want XDS to consider. Thanks! FR

[ccp4bb] Interpretation of wilson statistics and pseudosymmetry in R32.

Hi all I'm working on a structure of an RNA. Phases were obtained via SAD and the structure was refined to 21/26 % on R and R-free with a resolution of 2.8A, single molecule in the ASU. 7 residues were missing in a disordered loop out of a total of 54 residues in the asu. The cell was R32

[ccp4bb] Using SAXS data for phasing at mediocre resolution.

Hi all I'm looking for anyone who has had (practical) experience using SAXS data to phase 4.2 A crystals. Please email me. FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F

[ccp4bb] suggestions for SIR with strong diffraction anisotropy in the derivative

Hi all I'm trying SIR on my crystal both are C222. Native Cell Dimensions: 97.66 243.45 87.62 90 90 90 Resolution: 4.3 Derivative Cell Dimensions: 96.9100 244.66 87.61 90 90 90 Resolution: 4.7 . I plan to scale together using FHScal. Ctruncate says that my derivative has strong diffraction

[ccp4bb] strange pattersons

Hi All Im receiving some strange patterns in my pattersons. Space group is C222 with no confidence (due to resolution) of systematic absences to transform to C2221. Thanks! FR pattersonmap.pdf Description: Adobe PDF document - Francis Reyes

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

For a given reflection (h,k,l) how much does each situation increase the redundancy ? and which maximizes the ability to measure anomalous differences? (so assume we're separating friedel pairs here) a) measuring the same reflection again b) measuring a symmetry related reflection c) both

[ccp4bb] Heavy atom searching with disulfides

Hi all Has there been any work/reports of using disulfide restraints (number of heavy atoms as well as distance) for heavy atom searching/scoring for anomalous sulfur phasing? What resolution range would this be most effective? Thanks FR - Fra

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

Hi all I did some HA searching and found some sites in C222 that seem to be NCS related. Any ideas on how to determine whether or not the space group is really C2221 from these sites? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorad

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

s Nref Ncent FRCBIAS Nbias On 4 Aug 2009, at 09:47, Eleanor Dodson wrote: Cant you read the shell limits off the loggraphs? The numbers in the tables are given as 4sin**2/Lamba**2 I think but that is converted to As in the loggraph. Is that what you mean though? Eleanor Francis E Reyes

[ccp4bb] resolution shells for each bin in scala?

Hello ccp4'ers Where is / how can I obtain the resolution shell for each resolution bin in scala? My eyes can't seem to find it. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys

Re: [ccp4bb] Self Rotation map in R32?

>This nicely illustrates the danger of using too low resolution data to >compute the SRF (I'm referring to an earlier BB discussion on this >subject, where it was suggested to cut out the high resolution data, >against, it seems to me, all rationale). You should be using as high >resolution valid

Re: [ccp4bb] Self Rotation map in R32?

On Jul 21, 2009, at 7:50 PM, Charlie Bond wrote: By 'on the same scale' do you mean it is 40% of the height of the K=120 peak? Could it be a 'tail' of the kappa=120 degree peak? If you look at 95, 100, 110 etc does the peak persist and get stronger? I'm not sure how meaningful this would be

Re: [ccp4bb] Self Rotation map in R32?

ac.uk [mailto:owner- ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 21 July 2009 22:22 To: ccp4bb@jiscmail.ac.uk Subject: Self Rotation map in R32? Hi all I'm trying to understand why there is a peak that is perpendicular to the c axis on my kappa = 180 and kappa = 90? On the k

[ccp4bb] Self Rotation map in R32?

Hi all I'm trying to understand why there is a peak that is perpendicular to the c axis on my kappa = 180 and kappa = 90? The chapter entitled "Characterizing a Crystal From an Initial Native Dataset" from Sawaya says that R32 shouldn't have a central peak in kappa = 180 nor 90. Thank

[ccp4bb] Correction: [ccp4bb] molrep can't find *_trfn_scr.crd

reyes/ Andrea__121_molrep_/tmp/francisreyes/ Andrea_121_molrep_trfn_scr.crd " #CCP4I TERMINATION TIME 29 Jun 2009 11:10:51 #CCP4I MESSAGE Task failed Thanks FR Begin forwarded message: From: Francis E Reyes Date: June 29, 2009 11:15:14 AM MDT To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mo

[ccp4bb] molrep can't find *_trfn_scr.crd

When doing a multi-copy search, after the first rotation is done it seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp directory that it can't find just prior to doing the "first monomer search". Anyone have any ideas? thanks FR

[ccp4bb] Processing data as P1.

Say you have a case where the data is processed to a higher space group. This is done in mosflm ( by selecting '10 P4' for example after the auto indexing step), outputs an 'unmerged'.mtz which you subsequently merge/scale with scala (say to P41 21 2). However, you find that you might hav

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

Yes this is exactly what I wanted. I'm embarking on an educational pursuit of determining the space group from the diffraction images directly. Unfortunately it seems like all the solutions insofar are only commercially available as part of large packages that don't list their prices direc

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

Thanks all who replied. Looks like HKLView is it.. Oddly I couldnt find it anywhere in the ccp4i interface (shouldn't it at least appear under Program List)? FR On Jun 25, 2009, at 10:24 AM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photograph

[ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB

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

I have an R-free set for R32, I want to try scaling the data into say R3 or C2. How does one keep the R-free flags consistent? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

[ccp4bb] Clues to (perfect) twinning from the density map?

Hi all I know of a lot of reports that attempt to diagnose twinning from intensity distributions, however, are there reports that diagnosed (perfect) twinning from density maps? Strange unmodeled/modeled density? This is coming from a point of view that a perfectly twinned structure can

[ccp4bb] fortran format descriptor help

I've got a .cv from CNS that contains the following lines NREFlection= 5948 ANOMalous=TRUE { equiv. to HERMitian=FALSe} DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=FOBS

[ccp4bb] [offtopic?] putting b-factors from two pdbs on the same scale and interpretation

Hi all, Maybe this is more of a statistics/normalization question, but say you have the same molecule crystallized in two different states. How would you put their refined b-factors (directly from the pdb) on the same scale and say compare the b-factors of residues in the binding pocket?

[ccp4bb] low resolution scaling + merging... negative scales!

Hello all I've got a situation where I have a P321 space group to about 8.0A, it was able to scale and merge fine in hkl2000 but now I'm getting negative scales for Scala. Any suggestions on low resolution scaling and merging? Thanks FR - Franc

[ccp4bb] H3 to > 2.0A but low observations:parameter ratio

All It seems I have a case where I have 5595 reflections but my protein is about 102 residues. With a mean atom / residue * 4 parameters for each atom I get about 7833 parameters. So it seems that I have a observation : parameter ratio < 1. There is only 1 molecular per asu so there's no

[ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a dataset_name?

Despite setting a dataset name in the dialog box, i get the following in the log file. $TEXT:Warning: $$ comment $$ WARNING: PROJECTNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: CRYSTALNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: DATASETNAME not assigne

Re: [ccp4bb] Acrylamide in RNA crystallization

Are you talking about chunks of acrylamide? Or perhaps trace molecules? As for chunks, we normally pass it through a 0.2 um filter before setting up trays. FR On Apr 1, 2009, at 4:48 PM, vanessa delfosse wrote: Dear all, I'm currently trying to crystallize a 70 nt RNA and I would like to

[ccp4bb] GLRF and interpreting self rotation functions...

I am experimenting with GLRF and am having trouble calculating the locked self rotation function for a protein of known structure. The protein has a 3 fold NCS axis that is not parallel to a crystallographic axis. I'm at the step of specifying the local symmetry elements for the locked sel

[ccp4bb] Error with molrep when using locked srf.

Why do i keep getting an error when running molrep with locked rotation functions? Open failed: Unit: 8, File: /tmp/francisreyes/ qv_9_molrep_crossrot_alo.dat (logical: /tmp/francisreyes/ qv_9_molrep_crossrot_alo.dat) MOLREP(ccp4): Open failed: File: /tmp/francisreyes/ qv_9_molrep_crossr

[ccp4bb] PDB Submission of SAD data.

I have a mtz from Autosol/resolve that has the following columns: OVERALL FILE STATISTICS for resolution range 0.002 - 0.261 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs.

[ccp4bb] educational opportunity: Difference between SIRAS and SAD?

All Single isomorphous replacement with anomalous scattering uses two datasets that are isomorphous while using the anomalous signal in one (here scattering and dispersion are synonymous?). How does SIRAS use the anomalous scattering signal that's different than a single wavelength anomal

[ccp4bb] PyMOL: How to relax geometry constraints for cartoon mode/

I think this was posted earlier, but the geometry constraints for the cartoon mode is a little tight for a residue of my protein. What's the setting to relax them so it'll draw a continuous tube instead of leaving it blank? Thanks FR - Francis R

Re: [ccp4bb] screensaver [ or better yet, an automatically generated RSS feed]

Jürgen In the case you have an overwhelming amount of images, why not instead just setup an automatically generated RSS feed (on a server that you or maybe the ccp4 project or wiki will host) that contains them? There is an RSS screensaver already built into leopard, I'm sure there is on

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

It seems like this space group will be the death of me. I'm working on a structure in SG P41212 one molecule per asu that was solved with experimental SAD phases. The resolution is to 2.5 and the refinement is stuck at an R/Rfree of 30 and 33 with bonds rmsd of 0.011 and angles of 1.597 .

[ccp4bb] Obtaining relationships between two cross rotation solutions?

I have trouble with visualizing things in three dimensions so I'm trying to figure out the relationship between two cross rotation functions (given as theta1, theta2, theta3). Is there a program or webapp that'll tell me whether two rotation solutions are related by a 180/90/60/whathaveyo

Re: [ccp4bb] OT: VectorNTI alternatives

Not sure if it's been mentioned, but I personally use EnzymeX(http://mekentosj.com/enzymex/ ) . Also, I find their PDF library organizer Papers (http://mekentosj.com/papers/ ) to be exceptional. Cheers FR On Jan 28, 2009, at 1:47 AM, Darren Hart wrote: Hello, After several years of offering

Re: [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet...

There we have it then! Port everything to DirectX and use Vista ! ;) *shudder* Not to slam M$, but I run vista x64 at home and the hardware support is awful (manufacturers have yet to distinguish between driver support for 32 bit or 64 bit i.e. Vista capable on the box may mean only 32 bit

[ccp4bb] 3D 120hz LCD setups available

Since this was of discussion on this board a week or so ago, I figure it has relevancy. http://store.nvidia.com/DRHM/servlet/ControllerServlet?Action=DisplayProductDetailsPage&SiteID=nvidia&Locale=en_US&Env=BASE&productID=111286400&utm_source=newsletter&utm_medium=email&utm_campaign=store_Jan09

[ccp4bb] Crystallography plates, hanging drop but templated sealing film.

Does such a thing exist? A 24-well microplate configuration where in substitution of glass cover slips, you have a roll of tape templated such that there are circular areas where you can add your protein where there is no adhesive, but there is adhesive everywhere else? This may be a nightm

[ccp4bb] NonCCP4 - Screening xtals of light sensitive compounds?

Non CCP4 related! If you have experience screening for light sensitive compounds when xtals are obtained, can you send me a personal e-mail describing any tips,tricks, pitfalls, pointers? thanks FR - Francis Reyes M.Sc. 215 UCB University of Col

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 9:57 AM, Brian Mark wrote: Hi all, With all the talk about Mac OS X, I've not heard much mention about OS X Server and networking Macs together. Is anyone using the 10.5 server and LDAP to centrally house user directories on a RAID connected to a Mac server for exampl

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 11:41 AM, Anna S Gardberg wrote: 3. Eddie Snell made the point that most crystallographic software cannot take advantage of multiple processors yet. Still, as some people pointed, it is often convenient to try several refinement options at the same time, so there would

Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

Ironically as this stereo discussion ensues, it seems NVidia is pushing 3d glasses once again (http://tech.slashdot.org/tech/08/09/17/1530202.shtml ) . Those 120Hz LCD's are welcome reprieve from the bulky SGI monitors in our x-ray core now. More on topic, however, as a 'newer' generation (

[ccp4bb] Perfect twins.

Hello all, I believe I have a P41 perfectly twinned as a P41 21 2. I'm using the detwin_perfect.inp in CNS in every round of refinement to detwin the original P41 data as I update the single molecule in my asymmetric unit (so far). [1] Should I be able to find the second molecule (from re

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