[ccp4bb] Postdoctoral position in X-ray/EM at Birkbeck, University of London
Contact [EMAIL PROTECTED] or [EMAIL PROTECTED] for informal enquiries please do NOT reply to this email. Postdoctoral Research Assistant – Ref: 10082 School of Crystallography, Faculty of Science Full time, fixed term appointment for up to five years The School of Crystallography/Institute of Structural and Molecular Biology is seeking a Post-doctoral Research Assistant to carry out structural analysis of complexes of bacterial type IV secretion systems by cryo-electron microscopy. This project is funded by a programme grant from the Wellcome Trust to Prof Gabriel Waksman and is part of a collaboration with Prof Helen Saibil. The successful candidate will join the group of Prof Gabriel Waksman but will work in close collaboration with the Saibil group to determine the cryo-EM structure of type IV secretion sub-complexes. Further details on the research groups can be found at http://people.cryst.bbk.ac.uk/~ubcg54a/ and http://people.cryst.bbk.ac.uk/~ubcg16z/. Applicants should have a PhD in Structural Molecular Biology, Biophysics or a related area, postdoctoral research experience and relevant research publications. Salary range will be from £31,908 to £38,627 per annum inclusive of London Allowance on Grade 7 or 8, initial salary will be dependent on the skills and experience of the successful applicant. Closing date for completed applications: 20 June 2008 Go to https://www15.i-grasp.com/fe/tpl_birkbeckcollege01.asp?newms=jjid=24474; to apply for this post. If you have difficulties accessing this site please email, [EMAIL PROTECTED], quoting the appropriate reference in the subject header. Birkbeck is an equal opportunities employer and encourages applications from all candidates irrespective of gender, ethnicity, age, disability, religious belief and sexual preference. -- Dr Nicholas H. Keep Dean of Faculty of Science Reader in Structural Biology School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email [EMAIL PROTECTED] Telephone 020-7631-6852 (Room G57 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] Cis/trans double bonds in refmac/coot
I have a structure with an unsaturated lipid in the active site, which according to the chemists has one cis and one trans double bond. I would expect these to be controlled by the torsion angles in the cif files. However altering torsions between 0 and 180 makes no difference to the refinement and I get back what I put in terms of the fit of the molecule in coot. Coot is great for fitting such molecules into the density, but you can flip the cis-trans fairly easily. Is it correct that I just have to make sure the bonds are correct before starting refinement as the energy penalty for a cis/trans bond being wrong despite the torsion being set to a constant is simply too small? Best wishes Nick -- Dr Nicholas H. Keep Dean of Faculty of Science Reader in Structural Biology School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email [EMAIL PROTECTED] Telephone 020-7631-6852 (Room G57 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Cis/trans double bonds in refmac/coot
Dear Nic(holas), Nicholas Keep wrote: I have a structure with an unsaturated lipid in the active site, which according to the chemists has one cis and one trans double bond. I would expect these to be controlled by the torsion angles in the cif files. Yes, and a planar restraint (which is more converges faster). However altering torsions between 0 and 180 makes no difference to the refinement and I get back what I put in terms of the fit of the molecule in coot. That may very well be the case if you do not activate torsion angle refinement. Coot is great for fitting such molecules into the density, but you can flip the cis-trans fairly easily. Yes, I agree. Coot currently ignores const torsions (which is what I am guessing that you have for your trans bonds) in torsion refinement, I think, this is a mistake. BTW, It's much harder to cis-trans flip if you use hydrogens, I find. Is it correct that I just have to make sure the bonds are correct before starting refinement as the energy penalty for a cis/trans bond being wrong despite the torsion being set to a constant is simply too small? You *can* make coot fix up you cis-trans errors (and indeed prevent them from happening in the first place) but currently the interface is non optimal. You need to hand edit the const trans torsion restraints in the cif file so that the torsion id does not contain const and change sigma and period to 0.01 and 1 (say). (And you need to turn on torsion restraints, obviously (under the Refinement/Regularize Control button).) Paul.
[ccp4bb] Density Joining Cysteine and Lysine Side chains
Greetings. I'm wondering if anyone has ever seen something like this. I have a 2.1 A data set (synchrotron data) that is nearing completion. I see density that appears to join a cysteine side chain to a lysine (30 residues away from each other in primary sequence). There is a picture of the density here. http://labs.hwi.buffalo.edu/gulick/cyslys.html I have modeled this in as a Cysteine sulfenic acid (Side chain is Cb-Sg-OH) and refined. There remains a bit of positive Fo-Fc density above the oxygen and the lysine N and sulfenic acid hydroxyl are 1.8A away. I have some other crazy ideas but haven't been able to find any precedent in the literature. Any thoughts on what this might be or if anyone has seen something similar would be greatly appreciated. Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick
Re: [ccp4bb] Density Joining Cysteine and Lysine Side chains
Hi Andrew You don't say what your protein is crystallised in, or has seen during purification, but maybe S- MERCAPTOCYSTEINE might fit? (search for CSS in MSD CHEM) Do you have lower wavelength data that you might get a sulphur anomalous signal to check this? S-methyl Cysteine might fit as well - but the difference peak and bond lengths look more S-S than S-C. Hope this helps, Dave 2008/5/22 Andrew Gulick [EMAIL PROTECTED]: Greetings. I'm wondering if anyone has ever seen something like this. I have a 2.1 A data set (synchrotron data) that is nearing completion. I see density that appears to join a cysteine side chain to a lysine (30 residues away from each other in primary sequence). There is a picture of the density here. http://labs.hwi.buffalo.edu/gulick/cyslys.html I have modeled this in as a Cysteine sulfenic acid (Side chain is Cb-Sg-OH) and refined. There remains a bit of positive Fo-Fc density above the oxygen and the lysine N and sulfenic acid hydroxyl are 1.8A away. I have some other crazy ideas but haven't been able to find any precedent in the literature. Any thoughts on what this might be or if anyone has seen something similar would be greatly appreciated. Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
Re: [ccp4bb] Density Joining Cysteine and Lysine Side chains
...by lower wavelength, I mean longer wavelength... or lower energy. Take your pick. Dave 2008/5/22 David Briggs [EMAIL PROTECTED]: Hi Andrew You don't say what your protein is crystallised in, or has seen during purification, but maybe S- MERCAPTOCYSTEINE might fit? (search for CSS in MSD CHEM) Do you have lower wavelength data that you might get a sulphur anomalous signal to check this? S-methyl Cysteine might fit as well - but the difference peak and bond lengths look more S-S than S-C. Hope this helps, Dave 2008/5/22 Andrew Gulick [EMAIL PROTECTED]: Greetings. I'm wondering if anyone has ever seen something like this. I have a 2.1 A data set (synchrotron data) that is nearing completion. I see density that appears to join a cysteine side chain to a lysine (30 residues away from each other in primary sequence). There is a picture of the density here. http://labs.hwi.buffalo.edu/gulick/cyslys.html I have modeled this in as a Cysteine sulfenic acid (Side chain is Cb-Sg-OH) and refined. There remains a bit of positive Fo-Fc density above the oxygen and the lysine N and sulfenic acid hydroxyl are 1.8A away. I have some other crazy ideas but haven't been able to find any precedent in the literature. Any thoughts on what this might be or if anyone has seen something similar would be greatly appreciated. Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
[ccp4bb] Mosflm : data process of crystal with huge unit cell
Dear All I am processing data from a crystal for a large macromolecular complex with mosflm. Cell dimensions are around 120 x 150 x 650, with a p222 spacegroup. To avoid overlaps, we have collected data with a oscillation of 0.1 degrees. When I try to process the data with mosflm, mosaicity decreases along the processing to a very low values (0.05 to 0.1 depending on the images). The result is that I miss a lot of spots from the images. I would appreciate any help regarding : 1.- What's is the best strategy to process such a dataset ? 2.- Which are the critical parameters in mosflm to avoid these problems, and how to modify them ? 3.- and finally, can I use this data or your advice is to try to get crystals in a different spacegroup ? Many thanks Best regards Francisco - Francisco J. Enguita, Ph.D. Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] -
[ccp4bb] Microscope camera for taking crystal picture
Dear All, We are in the process of buying a new microscope with digital camera. Currently we are using MOTIC Digital Stereo Microscope (Model DMW-143-FBGG) with built-in CCD camera, but the quality of the crystal pictures is very poor. Furthermore the halogen light is quite hot. I would appreciate for any suggestion of brand/type microscope and digital camera purposely for taking good crystal pictures. Thanks. Regards Aida Aida Baharuddin, Ph.d Center for Chemical Biology, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, MALAYSIA.
Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell
Perhaps it should also be noted here that the long crystal axis should be oriented close to parallel to phi, in order to minimize overlaps. I have heard anecdotal evidence (anyone else?) that this long axis, in plate crystals, is usually normal to the surface of the plates. Perpendicularly-bent/folded loops, in combination with goniometer adjustments, can used to acheive this. The plate is then shot through the edge from all directions. Do others agree with this? It makes sense to me theoretically and in my own experience, anyway. Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, May 22, 2008 9:47 AM Subject: [ccp4bb] Mosflm : data process of crystal with huge unit cell Dear All I am processing data from a crystal for a large macromolecular complex with mosflm. Cell dimensions are around 120 x 150 x 650, with a p222 spacegroup. To avoid overlaps, we have collected data with a oscillation of 0.1 degrees. When I try to process the data with mosflm, mosaicity decreases along the processing to a very low values (0.05 to 0.1 depending on the images). The result is that I miss a lot of spots from the images. I would appreciate any help regarding : 1.- What's is the best strategy to process such a dataset ? 2.- Which are the critical parameters in mosflm to avoid these problems, and how to modify them ? 3.- and finally, can I use this data or your advice is to try to get crystals in a different spacegroup ? Many thanks Best regards Francisco - Francisco J. Enguita, Ph.D. Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] -
Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell
Dear Francisco, With a c axis of 650 Angs your phi-overlap problem is severe. When this axis is close to being parallel to the beam, the angular distance in radians between h,k,l and h,k,l+1 for a reflection hkl close to the top or bottom of an image is the angle spanned by c* viewed at a distance d* (=d*[h,k,l]), i.e. roughly c*/d*. This gives an angular distance of 1 degree for a c axis of 180 Angs at a resolution of pi (=3.14159...) Angs. In your case, at a resolution of 3.25 Angs this angular distance is only 1/200 radian, i.e. 0.286 degree; at higher resolution, it is proportionally smaller. Therefore, even a small mosaicity (0.2?) will give you severe phi overlap at the top and bottom of your images (assuming that the spindle axis is horizontal). The best you can hope for is that the estimation of that mosaicity by matching predicted spots to observed spots will give a correct rejection for affected reflections - until refinement against measurements that are linear combinations of intensities of several reflections, rather than intensities of individual reflections, becomes possible. With best wishes, Gerard. -- On Thu, May 22, 2008 at 03:47:24PM +0100, [EMAIL PROTECTED] wrote: Dear All I am processing data from a crystal for a large macromolecular complex with mosflm. Cell dimensions are around 120 x 150 x 650, with a p222 spacegroup. To avoid overlaps, we have collected data with a oscillation of 0.1 degrees. When I try to process the data with mosflm, mosaicity decreases along the processing to a very low values (0.05 to 0.1 depending on the images). The result is that I miss a lot of spots from the images. I would appreciate any help regarding : 1.- What's is the best strategy to process such a dataset ? 2.- Which are the critical parameters in mosflm to avoid these problems, and how to modify them ? 3.- and finally, can I use this data or your advice is to try to get crystals in a different spacegroup ? Many thanks Best regards Francisco - Francisco J. Enguita, Ph.D. Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] - -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell
Hi Francisco, you could try using these keywords in Mosflm: POSTREF WIDTH 3 #since you have 0.1 degree oscillation and Mosflm can only handle 30 images at once, the default I believe is 5 images if I'm not mistaken SEPARATION CLOSE PROFILE RMSBG 25 POSTREF USEBEAM Then I would start indexing from various images separated let say by 15 degrees use 6 or more if you have, don't go to full resolution first refine the cell estimate the mosaicity, fix the mosaicity and process a low res pass (what is your resolution ?). I assume you didn't run strategy beforehand and checked where you would have overlaps ? If you still have the crystal you could collect another dataset in a different orientation perhaps (assuming you can move kappa). I would then index on two images run strategy and get some images where the predicted overlaps are, then try to optimize the distance to the detector in favour of no overlaps. If you can, use the biggest CCD detector available or image plate if that has a larger detector area. Since you're in P222 you could also offset 2theta to artificially increase your detector area. Set the beam position almost at the edge of the detector and give your crystal a good 360 or more degree spin - sure you will end up with somewhere close to 100GB of data but who cares if you can solve the problem. 650 A is a challenge but not impossible - how many molecules in the asu do you expect ? Can you solve your problem with MR or do you need HA phases - if that is the case, then searching for another crystallization condition might be faster. Another thing to mention is if you have a homehexamer don't forget you can use NCS averaging so if you only collect a 2.5 A dataset your resulting electrondensity maps might look like 2 A after averaging. I suggest to rather be modest in resolution and have no overlaps then be able to solve the structure and go back eventually to optimize for higher resolution etc. With the cell dimensions you obtained you could startup XDS if you want to give it a try. As Graeme mentioned xia2 might be easier for a first time XDS user. Regarding obtaining new / different crystals you could try the Hampton additive screens with your crystal condition, with some luck you might end up with a more favourable crystal form and smaller cell dimensions. Assuming you are working on a macromolecular complex, do you have any EM information perhaps - then you would know if e.g. your cell dimensions correspond to one complex perhaps or more. Then the smallest cell axis you will most likely get will be in the size of your complex. Just some thoughts, Juergen [EMAIL PROTECTED] wrote: Dear All I am processing data from a crystal for a large macromolecular complex with mosflm. Cell dimensions are around 120 x 150 x 650, with a p222 spacegroup. To avoid overlaps, we have collected data with a oscillation of 0.1 degrees. When I try to process the data with mosflm, mosaicity decreases along the processing to a very low values (0.05 to 0.1 depending on the images). The result is that I miss a lot of spots from the images. I would appreciate any help regarding : 1.- What's is the best strategy to process such a dataset ? 2.- Which are the critical parameters in mosflm to avoid these problems, and how to modify them ? 3.- and finally, can I use this data or your advice is to try to get crystals in a different spacegroup ? Many thanks Best regards Francisco - Francisco J. Enguita, Ph.D. Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] - -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Finding NCS operator from one heavy atom site?
Hi, On Thu, May 22, 2008 at 11:22:19AM -0700, Juergen Bosch wrote: You can also scratch your head and look at the selfrotation function of your dataset. Some of that scratching can be done using GETAX for you - it's in CCP4 (for years), but hasn't got a CCP4i interface (yet: next release will have one). If you need help with that, please let me know ... We used GETAX once in about 1997 with a TaBr-cluster derivative (single site, phase information to about 7A) SIRAS, having 20 molecules/asu (2.5 D4 octamers) ... You do need to have a Cn/Dn local NCS though ... You might also try out using only the peak dataset (peak inflection) and see if the other wavelength actually harm your electrondensity, furthermore you could use Sharp to optimize your phases first. Yes, you want to start with the best density map possible :-) Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Finding NCS operator from one heavy atom site?
Hi Partha, ncs6d did really great things to me a while ago. Similar case as yours, only one Met site in each of the 4 monomers, pretty horrible maps. I was amazed how ncs6d could sort its way through the maps and find the ncs operators. As a simple approach I just took a spherical map around the methionine site. In fact it seemed to be easier to find the ncs between two dimers first, improve the operators with imp and then search for the missing operators within the dimer. Sorry, don't have any clever scripts for that, did it all by hand. The maps improve a lot after averaging. However, almost needles to say that cloning, expressing, purifying, crystallizing and solving the same construct of an 85% seq. identical ortholog took less effort than messing around with the bad maps... Good luck Jan 2008/5/22 Partha Chakrabarti [EMAIL PROTECTED]: Hi, Apologies for a non CCP4 question in strict sense. I am trying to work out the NCS operators for a three wavelength Se-MAD data which has only one site. The map is hardly interpretable. I came across the USF Rave package and what I am aiming is creak a mask around the heavy atom site (found by SHELX or Solve) using mama or so, (ideally from resolve.mtz but not necessarily), translate it to the other heavy atom site(s), give a 6d search with NCS6d and perhaps refine the best CC a bit with imp. If it works, I could try use the NCS operator in DM or Resolve etc. I was wondering if someone has a C-shell scripts for dealing with such situation already. Of course if there are other programs for such a task within CCP4, could give it a try. Best Regards, Partha
Re: [ccp4bb] Finding NCS operator from one heavy atom site? (long)
This almost does what you want, but not quite. To quote from the NCS6D manual: NCS6D uses a set of BONES or PDB atoms as input and tries to find a set of rotations and translations which maximise the correlation coefficient between the density at the (BONES) atoms and those at the same atoms after application of the operator. So you cannot use a mask in NCS6D - you can in IMP. In the case where I did something like this, I could see a single helix near the SeMet sites, so I built this helix, then used the following script to find the first NCS relationship: #!/bin/csh -f # /usr/local/Uppsala/rave_osx/osx_ncs6d EOF eden_400.ext P ncs6d_probe.pdb 1 p21212.sym 30.5 6.5 23.0 Y 0 359 10 0 179 10 0 359 10 -10 10 2 -10 10 2 -10 10 2 L rt_best.o EOF Then I wrote a little C program that broke out each of the 100-or-so NCS operators that are in rt_best.o into files called rt_test_NN.o (NN=integer) and ran each and every one of them through Imp: #!/bin/csh -f # # foreach file (rt_test_*.o) \rm LOG /usr/local/Uppsala/rave_osx/osx_imp MAPSIZE 3500 EOF ! LOG eden_400.ext model.mask p21212.sym $file Automatic 1. .02 2.0 .1 .01 .0001 2 Proper Complete Quit rt_test_new.o EOF set cc = `grep Correlation Coefficient LOG` echo $file echo $cc end # I guess you could create a fur ball of Calpha positions for the initial model to force NCS6D to sort of a volume average - or peak-pick the map around the Se sites - I have not tried this. I found that without the IMP step there were too many similar and unimpressive solutions for the NCS operator and the top one was not in general the correct one. This approach has the potential to consume quite a lot of CPU but the initial map was relatively ugly and ultimately it worked rather well. Others might have more elegant ideas. Phil Jeffrey Princeton Partha Chakrabarti wrote: Hi, Apologies for a non CCP4 question in strict sense. I am trying to work out the NCS operators for a three wavelength Se-MAD data which has only one site. The map is hardly interpretable. I came across the USF Rave package and what I am aiming is creak a mask around the heavy atom site (found by SHELX or Solve) using mama or so, (ideally from resolve.mtz but not necessarily), translate it to the other heavy atom site(s), give a 6d search with NCS6d and perhaps refine the best CC a bit with imp. If it works, I could try use the NCS operator in DM or Resolve etc. I was wondering if someone has a C-shell scripts for dealing with such situation already. Of course if there are other programs for such a task within CCP4, could give it a try. Best Regards, Partha
[ccp4bb] ccp4mg and speed
Hi all, ... tried on the ccp4mg bb before ... ccp4mg is such a nice program, yet it is so slow in my hands. An average sized map calculated from a mtz file takes about 30s to display, while coot displays both 2FoFc and FoFc maps in about 5s. Is there anything I can do to speed things up? I use: - ccp4mg-1.1.1-Linux-Fedora-Core - coot-Linux-i386-fedora-6 - python2.4 - Fedora Core release 6 Thanks a lot for any hints. Jan
[ccp4bb] SGI Dialbox on Coot/UCSF Chimera/ccp4mg/pymol
Hello, Does anyone know if any of these graphical softwares: COOT, UCSF Chimera, ccp4mg, PyMOL, accepts input from a sgi dialbox? And how to setup? We have just got one old SGI 8-dial box working on our linux PC (Fedora 8, x86_64). But it seems that only O responses to the input... Thanks in advance, Zhijie Li Biochemistry, U of Toronto
[ccp4bb] DDM artifacts?
Sorry for this non-CCP4 question, but I know no better venue to ask this: Do people see detergent spherulites or other artifacts in crystal screens in the presence of dodecyl-maltoside or other detergents? Are there any papers about this? I have seen some papers talking about the relationships between salt, temp, cmc, and cloud points, but nothing on precisely this topic (detergent-related crystallization artifacts). Best Regards, Jacob Keller ps. in passing, it seems like it would be a great idea to get together an excel database of all false-positive results (e.g. phosphate salt crystals) commonly found in the usual crystal screens. One could then search it to see whether one's current crystallization conditions have be villified in the past. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
[ccp4bb] angle restraint refmac etc
Dear All, I have a 3 minor questions re refmac internals: 1) does refmac use angle values directly or restrain 1-3 distances for angle restraint setup? 2) the ML coefficients FWT and DELFWT - are they the complete Fourier coefficients including the exponential, i.e. for example FWT = (2mFo-DFc)*exp(i*phwt)? (acc. to Murshudov Cie 1997 actad 53 p246 formula(20) they are). But I cannot reconcile that with what mtz2various does when it generates maps for xtalview. It writes hkl FWT and PHWT. This makes only sense when the ML coefficents FWT are only the 2mFo-DFc part excluding exp(i*phwt), because the FT computes FWT*exp(i*PHWT)*exp(-2Pihx). I think the equal sign in (20) is confusing. 3) what happens if 2mFo-DFc 0? Use |2mFo-DFc| and turn the phase around i.e. phwt=phic+180? Where could I find a reference for that? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] angle restraint refmac etc
On 23 May 2008, at 02:03, Bernhard Rupp wrote: Dear All, I have a 3 minor questions re refmac internals: 1) does refmac use angle values directly or restrain 1-3 distances for angle restraint setup? Yes. Angles are angles in degrees. 2) the ML coefficients FWT and DELFWT - are they the complete Fourier coefficients including the exponential, i.e. for example FWT = (2mFo-DFc)*exp(i*phwt)? (acc. to Murshudov Cie 1997 actad 53 p246 formula(20) they are). FWT (similarly DELWT) is amlitude of 2mFo exp(i phi_comb) - D |Fc| exp (i phi_c) and PHWT is the corresponding phase. But I cannot reconcile that with what mtz2various does when it generates maps for xtalview. It writes hkl FWT and PHWT. This makes only sense when the ML coefficents FWT are only the 2mFo-DFc part excluding exp(i*phwt), because the FT computes FWT*exp(i*PHWT)*exp(-2Pihx). Sign has already been taken into account I think the equal sign in (20) is confusing. 3) what happens if 2mFo-DFc 0? Use |2mFo-DFc| and turn the phase around i.e. phwt=phic+180? Where could I find a reference for that? Yes. But there is no reference. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
