[ccp4bb] strange P21 cell dimensions
Dear CCP4 and XDS users, I have a P21 case with some strange ratios in the cell dimensions : a, b=a, c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension and peak prompted me to think that the actual space group is side-centered. However in XDS any choice of such space groups receives bad scores. Could XDS be wrong in such a case ? Thank you in advance for your time, Peter.
[ccp4bb] FSEARCH question
Dear CCP4 users, I am trying to use FSEARCH to position a SAXS envelop in an attempt to solve a molecular replacement case. Could you explain what the x,y,z values in the output stand for. Do they represent the position of the center of mass of the molecule in the unit cell ? I would be grateful if you could shed some light on the matter, Peter
Re: [ccp4bb] ROSETTA for MR model generation
Hi Kornelius, A possible solution at this resolution would be to use Arcimboldo which localizes model fragments such as small helices with Phaser and then does density modification with SHELXE. See: Nature Methods 6:651-3. Crystallographic ab initio protein structure solution below atomic resolution Peter. On Wed, Aug 25, 2010 at 10:13 AM, Kornelius Zeth kornelius.z...@tuebingen.mpg.de wrote: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349 -- Peter
Re: [ccp4bb] No peak after self rotation function means...
Dear Marie, Look for peaks at your native Patterson map which might indicate pseudo-translation NCS that can not be detected by self-rotation. Peter. On Fri, Jul 16, 2010 at 10:04 PM, Marie Lacroix lacroix.ma...@rocketmail.com wrote: Hi everybody, I just calculated a self rotation function from the data used for molecular replacement (what by the way did not worked) and saw no peak at all. Does this not mean that there is only one molecule in the AU and no additional crystallographic axis? Matthews suggested 3-7 molecules. Sorry for this basic question, but I still have some problems with these self rotation functions, even when I see not one peak... Marie
[ccp4bb] Phased translation in MOLREP question
Dear All, I use MOLREP to fit my structure into various EM maps using phased rotation/translation. It works perfectly for some maps while for others it gets stuck in the translation search with the message : ERROR: in STRPACK: problem with memory allocation The EM maps that create this problem are actually smaller than those that do not. Thanks in advance for any suggestions as to what is wrong -- Peter
Re: [ccp4bb] SUMMARY: scala and xds data
Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take care of that and define cell parameters that fit best all data as scalepack does when it considers all separate frames , from all crystals where-as the input to XSCALE is not separate frames but complete datasets). Peter. On Sun, Apr 25, 2010 at 12:14 PM, Frederic VELLIEUX frederic.velli...@orange.fr wrote: Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil -- Peter
Re: [ccp4bb] SUMMARY: scala and xds data
Thank you for enlightening me and sorry for my ignorance, Peter. On Sun, Apr 25, 2010 at 5:33 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hi, I sense a misunderstanding: Cell parameters are not relevant when scaling together datasets: what matters are intensities and (depending on algorithm) directional cosines and the like. Cell parameters are relevant, along with the other experimental parameters, for knowing where to pick the intensities off the images (integrating). What denzo scalepack do (which I suspect you're referring to) is to split this into separate actions: denzo integrates, and scalepack postrefines, meaning it optimizes the integrated intensities by simultaneously taking into account experimental parameters over whole dataset. Only then does it scale. Xscale and Scala trust the intensities and only scale. Yes, the cell parameters are also an indicator that you may have non-isomorphism, but only that; it's the *intensities* where this is manifested. So you could have different cells yet still perfectly isomorphous intensities; or same cells and terrible non-isomorphism. phx. On 25/04/2010 16:05, Peter Grey wrote: Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take care of that and define cell parameters that fit best all data as scalepack does when it considers all separate frames , from all crystals where-as the input to XSCALE is not separate frames but complete datasets). Peter. On Sun, Apr 25, 2010 at 12:14 PM, Frederic VELLIEUX frederic.velli...@orange.fr wrote: Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil -- Peter -- Peter
Re: [ccp4bb] SUMMARY: scala and xds data
Hi Ingo, Scala might be beneficial after xds when several datasets need to be scaled together. Scala will refine cell parameters to fit best all the datasets together where as xscale uses as cell parameters those of the first dataset. If you use xscale you have to be prudent in your choice of the first dataset. Peter. On Sat, Apr 24, 2010 at 7:31 PM, Ingo Korndoerfer korndoer...@crelux.comwrote: as it turns out: the bad news (for me) 1. something went wrong in my data processing. point taken. yes. i was so hypnotized by the strange error message, that i did not realize this. the good news 2. pointless and scala run just fine (everybody can relax), and the strange messages are more an esthetic problem, that phil evans said he will fix in the next pointless release. had i looked at the pointless output i would have seen, of course, that my data are complete nonsense. embarassing ... thanks to phil for taking time to look over this, and thanks to the others who also replied and asked why i even scale xds data with scala rather than xscale. there are reasons for this, but the interesting news for me was, that it might be that xscale possibly delivers better data from xds than scala does, which, of course, now, i will have to look into ... time will tell ... greetings ingo -- Peter
[ccp4bb] Difference in results between v6.1.2 and v6.1.1
Dear CCP4 developers, I ran the same DM script (solvent flattening + averaging) in CCP4 6.1.2 and CCP4 6.1.1. There are differences in the results - not huge but significant. Could you please suggest a possible reason for that ? Thanks a lot, Peter.
[ccp4bb] Forcing same origin on different MR solutions
Dear crystallographers, I try to solve a MR problem in P21 with several different structures (and one EM map) as search models. I would like all solutions to have the same origin so I could compare them and see their relative positions. I think a possible solution is to bring the center of mass of all models (and map) to the same point. Is there another, easier, solution ? is there a way, already after molecular replacement, to bring all solutions to the same origin ? Thank you for your time, Peter
[ccp4bb] DMMULTI question
Dear CCP4 users, I am trying to improve MR phases using multi-crystal averaging in DMMULTI. First crystal has 3 fold NCS , 5A resolution and the second crystal no NCS , 4A resolution. I ask for your advice concerning two issues ; In the first cycle DMMULTI calculates solvent masks for the two crystals. Does it continously improve these masks or stick to the initial one ? Since DMMULTI does not apply gamma-perturbation (solvent flipping) should I use it to the highest common resolution (5A) only and continue with DM/PARROT to 4A ? Thank you for your time and advice, Peter
[ccp4bb] Histogram matching in DM - question
Hi everyone, I am trying to use density modification at rather low resolution (4-5A ) for an RNA structure. My first time ever with RNA. I usually use Histogram matching as part of the density modification scheme in DM. But this method is based on density distribution of protein maps I think. Is histogram matching still valid when it comes to RNA or protein/RNA structures ? And a general question regarding density modification and RNA structure. Can statistical density modification programs (RESOLVE, Pirate) take into consideration the chemical composition of the structure ? Shouldn't this composition affect the expected density distributions ? My gratitude in advance for your comments and advice, Peter.
[ccp4bb] Chainsaw question
Hi all, I attempt to create a suitable model for molecular replacement using CHAINSAW. Whenever the program needs to mutate a Proline into something other than alanine I get segmentation fault. This happens if the order of atoms in the proline residue is (N,CD,CA,CB,CG,C,O). Could you suggest how to solve this problem or alternatively how to change all prolines (there are many) to have another order of atoms which does not pose a problem to chainsaw (N,CA, C,O,CB,CG,CD) ? Thank you in advance for your advice, Peter.
