Re: [ccp4bb] FFT map coefficients only for certain chains
Like Herman, it was not apparent to me what exactly you want wanted. If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. Extensions - Maps... - Mask Map by Atom Selection, e.g. to show only the A chain, use an atom selection of //A. You can then export the map using: Extensions - Maps... - Export Map or Extensions - Maps... - Export Local Map Fragment... If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN). Paul. [1] use mask inversion [2] don't use mask inversion *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] High R factor
Dear Sir/Madam, I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] High R factor
Hi, it might well be possible that molrep used only lower resolution data (the default cutoff isd 2.5 A, if I remember correctly), when refmac uses all available data in the MTZ file... Check that both steps were performed at the same resolution ! Another possibility is that molrep performed the search in different spacegroups than the one specified in the MTZ file (eg P4 selected during data processing, and molrep checks, P4, P41, P42 and P43). If your solution corresponds to the P41 spacegroup, you have to modify your MTZ file (or use the one produced by molrep)... otherwise refmac will perform the rigid body step in P4 and not P41... This should be indicated in the molrep logfile... check it carefully ! hope this helps. If not please send the logfiles ! Laurent Le 20/02/2012 11:48, Dipankar Manna a écrit : Dear Sir/Madam, I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data. Please suggest. Regards Dipankar Manna This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] Scientist or Senior Scientist Position in China
Dear All, I would like to draw your attention to the following job vacancy in Jiangsu, P.R. China. Job ID Biortus_0131201201PS Posting Title Scientist or Senior Scientist, Structural Biology, Protein Structure Group Country P. R. China Work Location Jiangyin City, Jiangsu, P.R. China Company/Legal Entity Wuxi Biortus Biosciences, Inc. Posting Functional Area Research Job Type Full Time Employment Type Permanent Job Description Biortus Biosciences is an internationally recognized contract research organization (CRO) supporting small to large pharmaceutical companies around the world in the areas of protein expression and purification, structure based drug design, assay development, and medicinal chemistry. Biortus is equipped with strong research and development experience with capabilities to support these efforts. The successful candidate will lead a new centralized group responsible for generating protein or protein ligand complex crystal structures to expedite our clients’ drug discovery projects. Specifically, the candidate will design constructs for protein expression and purification, crystallization, data collection at home or synchrotron and structure determination. The candidate will also need to analyze the results, provide oral and written reports, and remain current with regard to literature reports and technological developments. Minimum requirements We are seeking a highly motivated and versatile PhD scientist or an MS scientist with 2+ years relevant experience to establish and lead a small structural biology group. Industry experience would be a distinct advantage, as would previous supervisory experience. A strong background in Biochemistry, Molecular Biology, Structural Biology or related field and have been well trained in protein and structural biology laboratories. The ideal candidate should have in-depth knowledge and hands-on experience in protein X-ray crystallography including crystallization, data collection, structure determination, refinement and analysis and must be familiar with characterizing protein-protein and protein-ligand interactions. The successful candidate must be detail oriented and be able to handle multiple tasks efficiently. The candidate must possess good communication skills and be comfortable working in a matrix based team environment. Please forward cover letter and CV to: j...@biortus.com
[ccp4bb] Postdoctoral Positions Available - Structural Biologist or Biochemist at UT Southwestern Medical Center
Postdoctoral positions are available for highly motivated scientists in the laboratory of Dr. Xin Liu at the University of Texas Southwestern Medical Center at Dallas (http://www.utsouthwestern.edu/fis/faculty/127166/xin-liu.html). The research of the laboratory is focused on the regulation of chromatin organization and its impacts on transcription and human diseases. We are particularly interested in elucidating the molecular and biophysical basis of chromatin dynamics including chromatin looping mediated by macromolecular complexes during transcriptional activation and repression. Applicants with background and interest in structural biology, protein and nucleic acid biochemistry, chromatin and transcription biology, or biophysical methodology are encouraged to apply. Candidates should submit a CV, a list of three references, and a brief statement of research accomplishments and career goals by e-mail to: xin@utsouthwestern.edu Xin Liu, Ph.D. Assistant Professor Cecil H. and Ida Green Center for Reproductive Biology Sciences Molecular Biophysics Graduate Program The University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Boulevard J7.104A Dallas, TX 75390-8511 Phone (office): 214-648-2493 Phone (lab): 214-648-4516 Fax: 214-648-0383 E-mail: xin@utsouthwestern.edu
[ccp4bb] Scientist or Senior Scientist Position in China
Dear All, I would like to draw your attention to a x-ray crystallographer position in Jiangsu, P. R. China. Best, Job ID Biortus_0131201201PS Posting Title Scientist or Senior Scientist, Structural Biology, Protein Structure Group Country P. R. China Work Location Jiangyin City, Jiangsu, P.R. China Company/Legal Entity Wuxi Biortus Biosciences, Inc. Posting Functional Area Research Job Type Full Time Employment Type Permanent Job Description Biortus Biosciences is an internationally recognized contract research organization (CRO) supporting small to large pharmaceutical companies around the world in the areas of protein expression and purification, structure based drug design, assay development, and medicinal chemistry. Biortus is equipped with strong research and development experience with capabilities to support these efforts. The successful candidate will lead a new centralized group responsible for generating protein or protein ligand complex crystal structures to expedite our clients’ drug discovery projects. Specifically, the candidate will design constructs for protein expression and purification, crystallization, data collection at home or synchrotron and structure determination. The candidate will also need to analyze the results, provide oral and written reports, and remain current with regard to literature reports and technological developments. Minimum requirements We are seeking a highly motivated and versatile PhD scientist or an MS scientist with 2+ years relevant experience to establish and lead a small structural biology group. Industry experience would be a distinct advantage, as would previous supervisory experience. A strong background in Biochemistry, Molecular Biology, Structural Biology or related field and have been well trained in protein and structural biology laboratories. The ideal candidate should have in-depth knowledge and hands-on experience in protein X-ray crystallography including crystallization, data collection, structure determination, refinement and analysis and must be familiar with characterizing protein-protein and protein-ligand interactions. The successful candidate must be detail oriented and be able to handle multiple tasks efficiently. The candidate must possess good communication skills and be comfortable working in a matrix based team environment. Please forward cover letter and CV to: j...@biortus.com
[ccp4bb] EMBO Practical Course: Computational structural biology - from data to structure to function
Hi all, In April we will once again organise the EMBO practical course on Computational structural biology - from data to structure to function. The application deadline is only a week away - 24 February. For more information about the course and how to apply, surf to: http://www.ebi.ac.uk/training/onsite/120416_structures.html --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] FFT map coefficients only for certain chains
Herman, Thanks for clarifying the difference between map coefficients and map files for me. What I really need are only map files, and I could generate those masked maps by following Paul's suggestion. Yu 2012/2/20 Paul Emsley paul.ems...@bioch.ox.ac.uk Like Herman, it was not apparent to me what exactly you want wanted. If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. Extensions - Maps... - Mask Map by Atom Selection, e.g. to show only the A chain, use an atom selection of //A. You can then export the map using: Extensions - Maps... - Export Map or Extensions - Maps... - Export Local Map Fragment... If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN). Paul. [1] use mask inversion [2] don't use mask inversion -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKCCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] real dimer vs crystal packing
Thanks, Artem! PDE2A also uses three domains to form a homodimmer. However, without the catalytic domain, the GAF B domain swings out. This is an excellent example for the restrictions set by the multidomain context. Anyone knows other examples? Thanks a lot! PDE2 full length versus domain only structures, I think. Artem On Thu, Jan 12, 2012 at 10:03 AM, Qiang Chen c...@red.dfci.harvard.eduwrote: Hi, I'm working on a multi-domain protein which uses three domains to form homodimer, and the full-length structure is available. We have solved the structure of one binding domain alone and found its homo-binding mode is totally different from that of the full-length protein. Do you know examples or papers discussing the similar subjects (crystal packing shows false binding mode)? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] Best method for weighted averaging of Friedel pairs?
This is a case where it is really helpful to keep some record of the unmerged integrated data. And again rejecting the odd outlier does no harm to most analyses.. I like to use scala to check for outliers looking at all i+ I- measurements; if there is a wild discrepancy for weak anomalous signals you have probably found an outlier which is best rejected. If you have a huge anomalous signal with good redundancy you probably shouldnt use Imean and the anomalous difference will be I= -I- with SD = sqrt (VarI+ VarI-). Most software which uses that signal will check for outliers in the Anom difference lists too, and it is usually safest to exclude them from anom site searches, and phase calculations. Eleanor On 14.02.2012 06:30, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Markus, why don't you reintegrate the data with hkl2000 telling the program to treat them as non-anomalous data-set? This should give you scalepack output with the Bijvoet pairs merged and overcome the problem you describe. Cheers, Tim On 02/13/2012 06:19 PM, Markus Meier wrote: On 11/02/12 02:52 PM, Bryan Lepore wrote: did you ever get a response on this? it is interesting but nobody posted publicly. -Bryan Dear Bryan, so far no one replied ... so please find my answer below. If someone disagrees, please post. None of the methods I have described are appropriate. If the negative Bijvoet mates and the positive Bijvoet mates have been merged separately to one intensity value for each (i.e. I+ or I-) plus the associated standard deviation (sigI+ or sigI-), any weighted method to calculate the mean will bias the intensity to either the I+ or the I-. Therefore the only appropriate method is to use the unweighted mean: Imean = 0.5*( I+ + I- ) sigImean = 0.5 * sqrt( sigI+^2 + sigI-^2 ) The only CCP4 program I found that actually does this is mtzMADmod. This method also has the advantage that the original intensity values of I+ and I- can be reconstructed from the mean and the anomalous difference (albeit with the loss of the original standard deviations). Method 1 (scalepack2mtz) should not be used. The resulting value is not the best estimate (maximum likelihood) Method 2 (in book by B. Rupp) gives the maximum likelihood average in case that the reflections are equivalent and is thus appropriate for the merging of the negative (or positive) set of Bijvoet mates, centric reflections (where the anomalous differences are zero) or in the case of an non-anomalous dataset the merging of symmetry equivalent reflections. Method 3 gives a more realistic sigma value in the case that the individual intensity values are far apart and their individual standard deviations are small. Consider the example I have posted: I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 Method 2: Imean=11738.95, sigIMean=244.31 Method 3: Imean=11738.95, sigIMean=7106.47 If the I+ and I- values above actually were symmetry equivalent reflections in an non-anomalous dataset, the sigImean from method 2 is ridiculously small and method 3 gives a far more realistic value. If method 3 is the best mathematical solution to this problem I am not able to judge and I have to trust the statistician (or programmer) who implemented this solution. Cheers, Markus On 10/02/12 01:47 PM, Markus Meier wrote: Dear all, I have a anomalous dataset, processed in HKL2000. Scalepack outputs a file containing the separately merged sets of the Friedel pairs I- and I+ and their standard deviations sigI+ and sigI-. Scalepack does not output the averaged intensities (Imean) and the standard deviations (sigIMean). The CCP4 program truncate that I use to convert the intensities to amplitudes requires Imean, I- and I+ and the respective standard deviations in its input file. I have now found at least three different methods to generate the averaged intensities from the Friedel pairs: 1) scalepack2mtz uses standard deviations for the weights: weights w = 1/sigI Imean = (w+*I+ + w-*I- ) / (w+ + w-) sigImean = 1 / (w+ + w-) 2) Method described in Biomolecular crystallography by Bernhard Rupp, p. 332/333 to average symmetry equivalent reflections uses variances for the weights: weight w = 1/sigI^2 Imean = (w+*I+ + w-*I- ) / (w+ + w-) sigImean = 1 / sqrt(w+ + w-) 3) Method used in cctbx function miller.set.average_bijvoet_mates() that calls generic merge.merge_equivalent_obs(): same as methods 2, except that sigImean is the larger of either a) sigImean = 1 / sqrt(w+ + w-) or b) sigImean = sqrt( wvariance ) where wvariance = (w+ + w-) / [ (w+ + w-)^2 - (w+^2 + w-^2) ] * [ w+*(F+ - Imean)^2 + w-*(F- - Imean)^2 ] What are the advantages and disadvantages of each method? Should method 1 be used at all? Some example from my dataset: Reflection (1, 1, 0), space group P3 2 1 I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 Method 1:
[ccp4bb] HKL2000 indexing problem
Hi all, I recently collected a data set off a single crystal and have had problems with indexing it. Every time I go pick peaks for indexing it constantly picks peaks that are just slightly off the actual peak. After indexing, it would always be that 2 of the 3 cell dimensions would be fairly normal, while the 3rd would have some impossible value such as 1. On some other occasions if it manages to pick peaks properly, and every time I go to index it, it gives back an error that I don't have enough peaks picked to index (picked nearly 500). I've tried using a number of different images to index from and have run into the same problem. Has anyone else run into these problems? Does anyone have any idea what might be wrong w/my dataset and/or crystal? Thanks in advance for any insight, Peter
Re: [ccp4bb] HKL2000 indexing problem
There could be many causes for this. Perhaps you do not have the best def.site file for your detector / beamline / hardware. What do your local HKL2000 experts tell you? You could e-mail me an image and I can help you. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Peter Hsu [hsuu...@u.washington.edu] Sent: Monday, February 20, 2012 6:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HKL2000 indexing problem Hi all, I recently collected a data set off a single crystal and have had problems with indexing it. Every time I go pick peaks for indexing it constantly picks peaks that are just slightly off the actual peak. After indexing, it would always be that 2 of the 3 cell dimensions would be fairly normal, while the 3rd would have some impossible value such as 1. On some other occasions if it manages to pick peaks properly, and every time I go to index it, it gives back an error that I don't have enough peaks picked to index (picked nearly 500). I've tried using a number of different images to index from and have run into the same problem. Has anyone else run into these problems? Does anyone have any idea what might be wrong w/my dataset and/or crystal? Thanks in advance for any insight, Peter
Re: [ccp4bb] choice of wavelength
The short answer is: no. Wavelength does not matter. Not for native data anyway. I wrote a paper about this recently. It is open access: http://dx.doi.org/10.1107/S0907444910007262 In particular, check out Figure 2. The two solid lines are pretty darn flat, and that means the wavelength dependence of damage and scattering power almost exactly cancel. More on the dotted lines in a bit... It is easy to screw up the scattering per damage calculation as there are many mathematical pitfalls. Perhaps the trickiest one is thinking that the longer detector distances that would be used at shorter wavelengths (keeping the resolution on the edge of the detector fixed) leads to a net reduction of background/spot. However, if you carefully calculate the area occupied by a spot, you again find that the noise due to background balances out, and there is again no wavelength dependence. Lots of people have made that mistake. Including me! But eventually I found the error. Some assurance can be hand that the no wavelength dependence conclusion is correct because experimental studies (http://dx.doi.org/10.1107/S0907444993013101), also found no significant wavelength dependence to signal/noise/dose, as expected. This is not to say that moving the detector back at constant wavelength is not a good idea. It is! You will generally get a signal/noise increase proportional to the distance (for weak spots). And yes, this is why we spend so much money on large-area detectors! Of course, the wavelength dependence of detector sensitivity is a completely different story. For most theoretical calculations you assume a perfect detector system where the only noise is photon counting (also called shot noise). It is important to remember that no such detectors actually exist. Even Pilatus has some calibration error, pile-up error, etc. as well as a finite capture fraction. In fact, pretty much any modern detector is designed to capture only 80-90% of the incident photons at most wavelengths. I could go on and on, but since the OP was only asking about 1.0 A vs 0.9 A, the change in detector performance over such a narrow range will be negligible when compared to things like crystal-to-crystal variation. Did you know that a 110 micron crystal is twice the volume of a 90 micron crystal? And therefore can absorb twice as much energy before enduring the same dose? The only other wavelength dependence that could be of practical importance is the escape of photoelectrons from the illuminated volume because these can carry away some energy that would otherwise cause damage. This build up region effect has long been a trick of medical dosimetry using MeV-class photons (Johns Cunningham, 1974). It was only recently demonstrated experimentally on an MX beamline 10.1073/pnas.1017701108. It may be possible to take advantage of this effect in a real-world data collection, but any real gain will require crystal volumes so small that you cannot get a complete dataset from just one. That is, unless you are working with VERY small molecules, you will need to be in the multi-crystal dataset regime before you can take advantage of photoelectron escape. So, for any regular native data collection, I'd say: no, wavelength doesn't matter. -James Holton MAD Scientist On 2/15/2012 3:55 PM, Bart Hazes wrote: Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy, so doubling the wavelength gives 8 times diffraction intensity, but only 4 times the signal on integrating detectors (assuming the full photon energy is captured). So it would be interesting to see how the equation works out on the new counting detectors where the signal does not depend on photon energy. Another point to take into account is that beamlines can have different optimal wavelength ranges. Typically, your beamline guy/gal should be the one to ask. Maybe James Holton will chime in on this. Bart On 12-02-15 04:21 PM, Jacob Keller wrote: Well, but there is more scattering with lower energy as well. The salient parameter should probably be scattering per damage. I remember reading some systematic studies a while back in which wavelength choice ended up being insignificant, but perhaps there is more info now, or perhaps I am remembering wrong? Jacob On Wed, Feb 15, 2012 at 5:14 PM, Bosch, Juergenjubo...@jhsph.edu wrote: No impact ? Longer wavelength more absorption more damage. But between the choices given no problem. Spread of spots might be better with 1.0 versus 0.9 but that depends on your cell and also how big your detector is. Given your current resolution none of the mentioned issues are deal breakers. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health
Re: [ccp4bb] Crystal Structures as Snapshots
Is it possible the solution structure of SAXS, NMR and EM neglect the existence of a very small percentage conformation of the molecule due to the overwhelming signals from the majority conformations? But this state of the molecule is trapped and enriched by the crystallization condition. Nian On Sat, Feb 11, 2012 at 1:10 PM, Poul Nissen p...@mb.au.dk wrote: Another good lesson here: 2. The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure.http://www.ncbi.nlm.nih.gov/pubmed/16364917 *Vestergaard B*, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M. Mol Cell. 2005 Dec 22;20(6):929-38. On 11/02/2012, at 18.18, Joel Sussman wrote: 2012_02_11 Dear All, Two really striking examples of Intrinsically Flexible Proteins are: (1) *Adenylate kinase*: Vonrhein, Schlauderer Schulz (1995) *Structure* *3*, 483 “Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases” *http://portal.uni-freiburg.de/structbio/structuregallery/ak_folder/mpeg* in particular look at: *video as MPEG white background, closing opening enzyme (707kb*) Each black dot [upper left, in the morph] indicates an observed crystal structure. (2) *Lac repressor*: see *Proteopedia* page on lac repressor, morphing from the structure bound to its cognate DNA, to that of the structure bound to its the non-cognate DNA, at:* http://proteopedia.org/w/Lac_repressor* best regards, Joel * * On 10 Feb 2012, at 22:51, Jacob Keller wrote: Interesting to juxtapose these two responses: James Stroud: How could they not be snapshots of conformations adopted in solution? David Schuller: How could that possibly be the case when any structure is an average of all the unit cells of the crystal over the timespan of the diffraction experiment? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] Modified and unmodified residue
Hello, I have a structure with a phosphorylated residue, but it looks like the residue may not be completely phosphorylated. I've currently modelled the residue purely as the phosphorylated variant, and have now been trying to put in a second conformer for the unmodified residue, but I'm finding the programs don't like two different residues with the same number. What is the best way to tackle this? Should I go back to normal residue designation and then make a link to the ligand? Does anyone have a link to help me do this? Thanks, Chris --- Dr. Christopher Wanty christopher.wa...@uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia
