Re: [ccp4bb] metal-chelating affinity chromatography and FosCholine detergents
Dear Pascal, There can be a number of reasons for this. Maybe fos-cholines are not very well suited for your membrane proteins of interest? - have you checked for activity or aggregation and compared to other detergents? If the detergent is optimal you may consider moving/extending the tag or changing it to the other terminus. Also: do you have enough column material? Have you tried to mix the resin and protein in batch instead of passing it on the column? Have you tried to recycle the load during binding? Poul On 13/07/2010, at 00.59, Pascal Egea wrote: > Dear All, > > I apologize for the not strictly crystallography-related query. > I am currently purifying several membrane proteins solubilized in > fos-cholines detergents and I consistently observe a significant loss of > protein at the binding step (done in absence of imidazole). Has anyone else > experience the same quite systematic (so far in my hands) problem with this > class of detergents. > I would appreciate any comments or advices from biochemists that face(d) the > same situation. > > Thanks in advance > > > -- > Pascal F. Egea, PhD > Assistant Professor > UCLA, David Geffen School of Medicine > Department of Biological Chemistry > 314 Biomedical Sciences Research Building > office (310)-983-3515 > lab (310)-983-3516 > email pe...@mednet.ucla.edu >
[ccp4bb] metal-chelating affinity chromatography and FosCholine detergents
Dear All, I apologize for the not strictly crystallography-related query. I am currently purifying several membrane proteins solubilized in fos-cholines detergents and I consistently observe a significant loss of protein at the binding step (done in absence of imidazole). Has anyone else experience the same quite systematic (so far in my hands) problem with this class of detergents. I would appreciate any comments or advices from biochemists that face(d) the same situation. Thanks in advance -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu
Re: [ccp4bb] Scaling two different mtzs
you can combine the two merged datasets with CAD and scale them together with Scaleit: see ccp4i -> Experimental phasing -> Data preparation -> Combine datasets with CAD, Scale and Analyse datasets Or you could give the unmerged files different dataset names, combine them in Pointless and scale them together in Scala, but that's probably not necessary Phil On 12 Jul 2010, at 21:53, Subhangi Ghosh wrote: > Hi All, > > I have two different datasets of the same protein, for example dataset A and > dataset B. I want to make a difference map of [ Fo (of set A) - Fo (of set > B)]. (I'll use phases of another solved structure from an isomorphous > crystal). For this I'll have to scale two different mtz files (associated > with set A and B respectively) but keep them separate after scaling. Is there > anyway that I can do this? > > Thank you, > Subhangi
Re: [ccp4bb] Scaling two different mtzs
Hi Subhangi phenix.fobs_minus_fobs_map will compute this map for you. Usage examples: phenix.fobs_minus_fobs_map f_obs_1_file=data1.mtz f_obs_2_file=data2.sca f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 model.pdb phenix.fobs_minus_fobs_map f_obs_1_file=data.mtz f_obs_2_file=data.mtz f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 phase_source=model.pdb high_res=2.0 sigma_cutoff=2 Or (using the GUI): Maps -> Isomorphous difference maps. Note, both inputs MTZs should have similar crystal symmetry. Let me know if you have questions. Pavel. PS> This is a non-CCP4 tool. On 7/12/10 1:53 PM, Subhangi Ghosh wrote: Hi All, I have two different datasets of the same protein, for example dataset A and dataset B. I want to make a difference map of [ Fo (of set A) - Fo (of set B)]. (I'll use phases of another solved structure from an isomorphous crystal). For this I'll have to scale two different mtz files (associated with set A and B respectively) but keep them separate after scaling. Is there anyway that I can do this? Thank you, Subhangi
Re: [ccp4bb] Beamtime at the ALS-BCSB beamlines
Sorry for the clutter: This is of course for the Aug/Sept cycle. P 2010/7/12 Peter Zwart > Dear All, > > July 15, 2010 is the deadline for the March/April 2010 Rapid > Access Proposal cycle. > > All Berkeley Center for Structural Biology(BCSB) beamlines are equipped > with ADSC Q315/Q315R detectors, automated sample changers and data > collection software enabling high-throughput crystal screening and data > collection. > > Remote data collection is available on all BCSB beamlines, providing > the user with the full complement of sample visualization, sample > manipulation, beamline control, data acquisition and data analysis tools > exactly as they would see them if they were stationed at the beamline. The > main difference between local operation and remote operation, is the length > of the network cable! This enhanced remote operation capability is coupled > with 22hr onsite support by BCSB staff who are able to assist immediately > with loading additional samples for remote users or troubleshoot any issues > that might arise. Remote users can furthermore be kept up-to-date on > changes in ring status via an SMS service ( > http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone) > or via twitter (@AlsRingStatus). > > Specific features are summarized below. > > > Beamlines 5.0.1, 5.0.2, 5.0.3: > -- > > Beamline 5.0.2 is equipped with a novel variable collimator allowing users > to adjust the beamsize continuously and on the fly between 25 and 100 > micron, both horizontally and vertically. With a collimator setting of 30x30 > micron, typical exposures are around 1 to 2 second. > > The Berkeley Automounter sample handling system has a routine capacity of > 96 samples (6 pucks). In a typical high-throughput screening mode, the > mount-to-mount time is around 2.5 minutes per sample, allowing users to > screen a full puck within 45 minutes. > > The sector 5 beamline user stations are equipped with > fully high-adjustable, ergonomically friendly work stations. > > > Beamlines 8.2.1 and 8.2.2: > --- > > To facilitate studies on small crystals, a microdiffractometer > was installed in the beamline 8.2.1 endstation. The new equipment > allows precise sample positioning to within 2 microns, excellent > sample viewing of very small crystals, and an off-axis crystal > positioningstage. > > Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer > (Actor), allowing remote operations to now be a routine mode of access > for these beamlines. > > > Data analyses in the BCSB is facilitated by software maintained by sbgrid ( > http://www.sbgrid.org). A 16 core linux machine is available for our > users to process their data and solve/refine their structure. > > An additional mode of access to the BCSB beamlines is through > the Collaborative Crystallography (CC) Program. Users apply for beamtime via > the general user program, and collaborate with an expert crystallographer > who will conduct the experiments and data reduction on behalf of the > researchers. Depending on the users, structure solution, model building and > refinement can be carried out as well. Please contact > bcsbbeamt...@lbl.gov for more information. > > Please visit http://bcsb.lbl.gov/ for more details about the Center and > its beamlines. > > To find out more, click on: > > http://www.als.lbl.gov/als/quickguide/independinvest.html > > We invite you to submit a proposal at: > > http://alsusweb.lbl.gov/ > > Scroll down to "Structural Biology beamines (includes protein SAXS)." > > Click on "New Proposal." > > If you have any questions or would like to request open beamtime, > please e-mail bcsbbeamt...@lbl.gov. > > Please note that executed user agreements must be received by LBNL > prior to beamtime. Proprietary fees, if applicable, must be received > by LBNL at least five working days prior to scheduled beamtime. > > > -- > - > P.H. Zwart > Research Scientist > Berkeley Center for Structural Biology > Lawrence Berkeley National Laboratories > 1 Cyclotron Road, Berkeley, CA-94703, USA > Cell: 510 289 9246 > BCSB: http://bcsb.als.lbl.gov > PHENIX: http://www.phenix-online.org > SASTBX: http://sastbx.als.lbl.gov > - > -- - P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -
[ccp4bb] Scaling two different mtzs
Hi All, I have two different datasets of the same protein, for example dataset A and dataset B. I want to make a difference map of [ Fo (of set A) - Fo (of set B)]. (I'll use phases of another solved structure from an isomorphous crystal). For this I'll have to scale two different mtz files (associated with set A and B respectively) but keep them separate after scaling. Is there anyway that I can do this? Thank you, Subhangi
Re: [ccp4bb] Coot binary for Ubuntu 10.04 64 bit
I just compiled the latest coot (0.6.2-pre-1.3011) on 64-bit Lucid (it appears that the gtkglext issue is gone). I don't know what you mean by so many compiling issues. Are you using autobuilder script? On Sun, 2010-07-11 at 12:28 -0700, Michael Hothorn wrote: > Hi, > > can someone point me to a recent coot binary that runs under Ubuntu > 10.04 64 bit? There are so many compiling issues that I am about to give > up compiling it myself > > thanks! > Michael -- Coot verendus est
[ccp4bb] Beamtime at the ALS-BCSB beamlines
Dear All, July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. The main difference between local operation and remote operation, is the length of the network cable! This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service ( http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone) or via twitter (@AlsRingStatus). Specific features are summarized below. Beamlines 5.0.1, 5.0.2, 5.0.3: -- Beamline 5.0.2 is equipped with a novel variable collimator allowing users to adjust the beamsize continuously and on the fly between 25 and 100 micron, both horizontally and vertically. With a collimator setting of 30x30 micron, typical exposures are around 1 to 2 second. The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Beamlines 8.2.1 and 8.2.2: --- To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Data analyses in the BCSB is facilitated by software maintained by sbgrid ( http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact bcsbbeamt...@lbl.govfor more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you have any questions or would like to request open beamtime, please e-mail bcsbbeamt...@lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- - P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -
[ccp4bb] July 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The deadline for Sep/Oct 2010 Collaborative Crystallography proposals will be *July 15, 2010. * Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography - How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Sep/Oct 2010 allocation period, proposals must be submitted by *July 15, 2010.* The deadline for CC proposals for the time period Nov/Dec 2010 will be Sep 15, 2010. Regards, Banumathi Sankaran
[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for researchers and students interested in structural biology. At its center is the PDB archive – the sole international repository for the 3-dimensional structure data of biological macromolecules. These structures hold significant promise for the pharmaceutical and biotechnology industries in the search for new drugs and in efforts to understand the mysteries of human disease. The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB processes, stores, and disseminates these important data, and develops the software tools needed to assist users in depositing and accessing structural information. The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has one opening for a Biochemical Information & Annotation Specialist to curate and standardize macromolecular structures for distribution in the PDB archive. The annotation specialists validate, annotate, and release structural entries in PDB archive. The annotation specialists also communicate daily with members of the deposition community. The position is an academic position with state benefit. The salary is compatible with faculty level. A background in macromolecular crystallography or small molecule crystallography is a strong advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, biological databases is preferred. The successful candidate should be self-motivated, pay close attention to detail, possess strong written and oral communication skills, and meet deadlines. This position offer the opportunity to participate in an exciting project with significant impact on the scientific community. Please send resume (pdf preferred) to Dr. Jasmine Young at pdbj...@rcsb.rutgers.edu. -- Jasmine Young, Ph.D. RCSB Protein Data Bank Assistant Research Professor Lead biocurator Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: jas...@rcsb.rutgers.edu Phone: (732)-445-5497 Fax:(732)-445-4320
Re: [ccp4bb] Beginning crystallography text
For all those who asked about the new edition of the Sherwood book, it is available for pre-order on Amazon (at least on the UK version, search for "Crystals, X-rays and Proteins: Comprehensive Crystallography"). Simon PS Jon - do I get a commission? On 12 Jul 2010, at 11:28, F.Xavier Gomis-Rüth wrote: Could you please let us know when it appears ? A message to the ccp4bb would be really very much appreciated. Best, Xavier Simon Kolstoe escribió: FYI an updated version of the Sherwood book will hopefully be published in the next few months. Simon On 10 Jul 2010, at 18:04, Vineet Gaur wrote: Hi, I found "Crystal, X-rays and Proteins" by Dennis Sherwood very helpful in understanding the basic concepts of crystallography. However, it seems that the book is out of print. It would be great, If anyone here is having an E-copy of this book and can share with us. Thanks, Vineet --
[ccp4bb] Post-doc position available at the Sanford-Burnham Institute
Postdoc: Protein Biochemistry, Protein Crystallography and Drug Discovery We hare recruiting a Postdoctoral Associate in the area of nuclear hormone receptor biology and structural biology to join the Rastinejad lab at the SanfordâBurnham Medical Research Institute in Orlando, Florida. The responsibilities will be to express members of the nuclear receptor family of proteins and to conduct biochemical and cell-based assays searching for novel ligands, and to use protein crystallography / X-ray diffraction to understand stero-specific interactions. Applicant is expected to have solid previous background in the areas of cloning, protein expression and isolation, and with additional experience in X-ray crystallography. Applicants: please make sure to forward 2-3 names for letters of reference from persons knowledgeable with your prior experience in science, together with your C.V. and cover letter to Ms. Stephanie Dickstein eâmail address: sdickst...@burnham.org
Re: [ccp4bb] A strange case of MR
Given your unit cell parameters + high Rsym I'd say you have an indexing problem. If you try P2, what happens? I suspect that you might have something as simple as incorrect beam center position and while integration works, scaling fails (the only way you are getting away with it is by choosing P1 ans thus low redundancy). Show us your scaling statistics. Some programs are more sensitive than others to incorrect beam center, your best bet is to try something like Labelit and verify that you are using correct values. On a diffraction pattern, sometimes you can identify rings of reflections, one of them may pass through the beam center. What software you are using for data processing? On Mon, 2010-07-12 at 11:00 +0800, 孙庆祥 wrote: > Dear ccp4 experts, > > I'm a beginner and have a problem with the following structure > solution. I need great help from you experts. Thanks in advance! > > The dataset is 1.6A resolution and the spots looks ok, except some > smear in the higher resolution. Space group is P1(could be P2 or P21). > Completness is above 95% and mosaicity is less than 1. Rsym is 0.6. > > Cell parameters are: a=18.2320 b= 39.6330 c=77.5260 alpha=104.8230 > beta=90.0780 gamma=90.0400 > > The model is about 60 amino acids snake venom protein with 60% > identity. However, no solution with an initiall R less than 0.7 was > obtained by Molrep, Phaser, or Phenix . > > Using a molrep search result (R=0.75, mtz in P1, 2 moelcules in > AU), with Refmac5 twin refinement, we could refine the structure to > 40% Rfree and 38%Rwork. The density looks good (can see hole in rings > structures) for all residues and no continous unexplained density is > observed. However, the R and Rfree does not go down no matter what we > try... > > We tested the twinning by CNS or the crystal twinning server > (http://nihserver.mbi.ucla.edu/Twinning/) and found no twinning > present. > > I'm sure the sequence is correct. > > I've tried hard on this for quite some time. Really appreciate if you > could help. > > Thanks and regards, > > Jeremy > > > -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
Re: [ccp4bb] problem updating job status
Dear Sebastien,
A first guess is that the script is only familiar with english dates.
You could try to type
export LC_ALL="C"
in the terminal just before you start ccp4i from that same terminal to see if
that improves anything.
This syntax is correct for POSIX shells (bash, ksh, zsh,...). In case you are
using csh, you'd have to ask someone familiar with csh ( and consider
changing to a POSIX shell ).
Cheers, Tim
On Mon, Jul 12, 2010 at 03:34:43PM +0200, Sebastien Moniot wrote:
> Dear all,
>
> Since a couple of weeks, and I believe the update of my machine to Ubuntu
> 10.04 Lucid Lynx 64, I'm experiencing problems with the ccp4i job status.
> For some reasons it cannot update to FINISHED status even if the job works
> out fine. The update to version 6.1.13 didn't succeed.
> Pasted below is the error message I got :
>
> unable to convert date-time string "12 juil. 2010 15:22:35"
> unable to convert date-time string "12 juil. 2010 15:22:35"
> while executing
> "clock scan $date"
> (procedure "ReportJobFinish" line 35)
> invoked from within
> "ReportJobFinish $logfile status time output_files"
> (procedure "DbUpdateStatus" line 16)
> invoked from within
> "DbUpdateStatus "
> ("after" script)
>
> Does anyone would know how to fix this ?
>
> Sebastien
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
signature.asc
Description: Digital signature
Re: [ccp4bb] DNA pdb format problem when using CNS
Hi Hongjun Yu, In CNS you need to change the name of the DNA base like this: DG -> GUA DC -> CYT DT -> THY DA -> ADE and for the thymine make sure to change the atom C7 into C5A and it should work with CNS. Good luck, Pierre Pierre Aller Ph.D. Postdoctorate Associate University of Vermont 201 Stafford Hall 95 Carrigan drive Burlington, VT 05405-0084 Phone: 802-656-9534 mailto:pierre.al...@uvm.edu
[ccp4bb] problem updating job status
Dear all,
Since a couple of weeks, and I believe the update of my machine to Ubuntu
10.04 Lucid Lynx 64, I'm experiencing problems with the ccp4i job status.
For some reasons it cannot update to FINISHED status even if the job works
out fine. The update to version 6.1.13 didn't succeed.
Pasted below is the error message I got :
unable to convert date-time string "12 juil. 2010 15:22:35"
unable to convert date-time string "12 juil. 2010 15:22:35"
while executing
"clock scan $date"
(procedure "ReportJobFinish" line 35)
invoked from within
"ReportJobFinish $logfile status time output_files"
(procedure "DbUpdateStatus" line 16)
invoked from within
"DbUpdateStatus "
("after" script)
Does anyone would know how to fix this ?
Sebastien
Re: [ccp4bb] Off-topic: crystallization after refolding
However, treatment with urea is known to modify proteins (N-term/Lys/Arg), which could ultimately effect crystallization. Is this something that people generally worry about? For example -would you bother cleaning up the urea by ion exchange -get ultra pure urea (ultra $$$) -change to guanidinium chloride -hope that it might benefit crystallization (i.e. similar to methylation of lysines) Have ~ 50 mM glycine or tris in your urea solution and prepare it fresh. Then you don't have to worry about carbamylation. Dima
Re: [ccp4bb] Off-topic: crystallization after refolding
Try first to give it a shot and see if you get crystals without too much hassle and expense. I would recommend a size exclusion chromatography step after refolding and from that collect a uniform sample for crystallization. Poul On 12/07/2010, at 13.39, meindert lamers wrote: > Dear all, > > I can get large amounts of a protein that is purified from inclusion bodies. > The protein is solubilized using 6M urea and refolded by dialysis. > > However, treatment with urea is known to modify proteins (N-term/Lys/Arg), > which could ultimately effect crystallization. > > Is this something that people generally worry about? > For example > -would you bother cleaning up the urea by ion exchange > -get ultra pure urea (ultra $$$) > -change to guanidinium chloride > -hope that it might benefit crystallization (i.e. similar to methylation of > lysines) > > > Thanks in advance, > Meindert > > > -- > ** > Meindert H. Lamers > Medical Research Council > Laboratory of Molecular Biology > Hills Road, > Cambridge, CB2 0QH > United Kingdom > tel +44 (0)1223 402401 > fax +44 (0)1223 213556 > web: http://www2.mrc-lmb.cam.ac.uk/groups/mlamers/ > **
[ccp4bb] Off-topic: crystallization after refolding
Dear all, I can get large amounts of a protein that is purified from inclusion bodies. The protein is solubilized using 6M urea and refolded by dialysis. However, treatment with urea is known to modify proteins (N-term/Lys/Arg), which could ultimately effect crystallization. Is this something that people generally worry about? For example -would you bother cleaning up the urea by ion exchange -get ultra pure urea (ultra $$$) -change to guanidinium chloride -hope that it might benefit crystallization (i.e. similar to methylation of lysines) Thanks in advance, Meindert -- ** Meindert H. Lamers Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH United Kingdom tel +44 (0)1223 402401 fax +44 (0)1223 213556 web: http://www2.mrc-lmb.cam.ac.uk/groups/mlamers/ **
[ccp4bb] DNA pdb format problem when using CNS
Hi, I am refining a protein complexed with a modified DNA(cordinates obtained from published structure) with CNS. But I am stuck with the pdb format problem. I followed the tutorial on CNS website and the first step just went wrong when command 'fix_dna_rna' didn't work. I also tried the normal DNA cordinates generated from web server 'make-na', it went on very well. Comparing the two pdb cordinates makes me believe the pdb format does matters. But I still don't know the rules of pdb version and can't find full description from the web. So I ask help here. Any advice (program recommendation or how to change the atom manually) would be very helpful. best regards, Hongjun yu
Re: [ccp4bb] A strange case of MR
Have you used pointless to examine possible spacegroups? It is possible to get one lattice point out and get a very high rsym pointless will check these possibilities for you The cell could be this: C m m m 39.6 149.9 18.2 89.9 90.0 90.0 0.10 [-k,-k-2l,h] You need to go back to the processing step I think.. Eleanor Poul Nissen wrote: You mention that your Rsym is 0.6 - this seems outrageously high (except if the 0.6 is just for your outer resolution bin). If 0.6 is indeed the overall Rsym you have a basic problem of unit cell and space group assignment to reconsider. Check if your processing accounts for all spots and check the input beam position - if its wrong you may have mis-indexed by one (e.g. on l, corresponding to the longest axis of your unit cell - c) Later on: if you have any sulphurs in the structure you might consider sulphur-SAD to complement your MR. Let the MR find your S positions and go from there. Poul On 12/07/2010, at 05.00, 孙庆祥 wrote: Dear ccp4 experts, I'm a beginner and have a problem with the following structure solution. I need great help from you experts. Thanks in advance! The dataset is 1.6A resolution and the spots looks ok, except some smear in the higher resolution. Space group is P1(could be P2 or P21). Completness is above 95% and mosaicity is less than 1. Rsym is 0.6. Cell parameters are: a=18.2320 b= 39.6330 c=77.5260 alpha=104.8230 beta=90.0780 gamma=90.0400 The model is about 60 amino acids snake venom protein with 60% identity. However, no solution with an initiall R less than 0.7 was obtained by Molrep, Phaser, or Phenix . Using a molrep search result (R=0.75, mtz in P1, 2 moelcules in AU), with Refmac5 twin refinement, we could refine the structure to 40% Rfree and 38%Rwork. The density looks good (can see hole in rings structures) for all residues and no continous unexplained density is observed. However, the R and Rfree does not go down no matter what we try... We tested the twinning by CNS or the crystal twinning server (http://nihserver.mbi.ucla.edu/Twinning/) and found no twinning present. I'm sure the sequence is correct. I've tried hard on this for quite some time. Really appreciate if you could help. Thanks and regards, Jeremy
Re: [ccp4bb] Twin questions: is my crystals twinned or not?
There isnt much evidence for twinning that I can see. Moments sensible, Ltest sensible for untwinned data, some distortion of the cumulative intensity plot but that could be due to integration problems. Comparing Rfree in P3 is only proper if you have kept the same FreeR set as you assigned in P321. So I think you probably should stay with P321. Eleanor Parthasarathy Sampathkumar wrote: Dear All, Back ground: This is my first experience with a twined dataset. Crystals belong to a small domain of 132 aa, out of which ~40 residues appears to be disordered (~30 of those from C-terminal and C-term His6 tag). Initial space group: P3 with unit cell dimensions: 62.507 62.507 55.117 90.00 90.00 120.00; Resolution 2.35Angs. Pointless suggested P321 (space group # 150) as possibility. I determined structure by MR with Phaser (1 molecule in ASU). After several model building and refinement cycles R and Rfree got stuck at 24.0% and 31.6% respectively. Therefore, I considered P3 space group (now Two molecules in the ASU) with a twin component. I was only able to add handful residues to the model already refined in P321. My current R and Rfree factors are 21.0% and 29.1%, respectively for Two molecules refined in P3 space group. Questions: 1. H-test in cTruncate suggested a twin fraction of 0.43 for the twin operator -h-k, k, -l. Where as Refmac5 with Amplitude based twin refinement gave an initial value of 0.508 for the same operator. Why these values are different between cTruncate and Refmac5 (is this because I asked Refmac5 do amplitude Twin refinement instead of Intensity based)? 2. I noticed in Refmac5 log file that twin fractions changes for every cycle of refinement. During my most recent Refmac5 run Initial estimate of 0.508 for -h-k, k, -l operator changed to 0.504 at the end of 20th cycle. The corresponding values were 0.519 and 0.529, respectively, in a previous round. Since twin estimates were based on measured Intensities (in turn amplitudes) why would they change with refinement (am I missing something here)? 3. When I repeated my final round of Refmac5 WithOut Twin Refinement my R and R-free factors are 22.9% and 28.6%, respectively, which also appears to be OK for 2.35 Angs. data (in fact, slightly better R-free). These values are likely to improve little bit after completing the solvent model. So, is this crystal really twinned? I have attached log files of cTruncate and most recent Refmac5 run with Twin refinement. Apologies for attachments (at least no image files). Thank you all in advance for educating me. -Partha
