Re: [ccp4bb] Wilson plot from truncated.mtz
You're right F^2 != F^2 It wouldn't be hard to get Truncate to output F^2 as well One reason why I've got rid of the Is in mtz files myself is just to save space (less important these days), particularly if I knew I wasn't going to use them. If we add F^2 then we have for each dataset F, Dano, F+, F-, Imean, I+, I-, F^2mean, F^2+, F^2- each with a sigma, + ISYM, 21 columns in all This can get confusing and used to (at least) hit some limits if you had lots of derivatives or wavelengths Phil On 24 Aug 2008, at 21:12, Ian Tickle wrote: Phil Squaring the F (i.e. the best estimate of Ftrue) that Truncate estimates does not give you F^2 (the best estimate of Itrue): F = Integral[0:infinity] sqrt(J) p(J|I) dJ var(F) = Integral[0:infinity] (sqrt(J)-F)^2 p(J|I) dJ F^2= Integral[0:infinity] J p(J|I) dJ var(F^2) = Integral[0:infinity] (J-F^2)^2 p(J|I) dJ where p(J|I) = p(I|J) p(J) / p(I) [Bayes Theorem] and I = Imeas, J = Itrue. From the eqn for var(F) we see that var(F) = F^2 - F^2, or F^2 = F^2 + var(F), i.e. F^2 is not the same as F^2. If you want to use the true F^2 in a calculation, isn't F^2 the best estimate by definition? Using Imeas in a calculation where Itrue is called for is exactly equivalent to assuming a uniform Bayesian prior p(J) on Itrue, i.e. you're assuming that all true values of I (constrained at least to be = 0 by physics and constrained further by the assumed distribution of atom positions) from -infinity to +infinity are equally likely!! - so you're throwing away all prior knowledge about the data. It doesn't seem logical to make use of prior info to estimate F but then not use it to estimate F^2. By using F^2 wouldn't you be making the best use of your prior knowledge? Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: 24 August 2008 20:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Wilson plot from truncated.mtz You're right. The smoothed I is used for the Truncate procedure, though it is difficult in the very low resolution bins. Also it doesn't allow for pseudo-translations, which it should. As you say, the linear fit is only used to put data on a very rough absolute scale. This isn't necessary, but it doesn't hurt There's no reason why truncate shouldn't give a best estimate of |F| ^2 but I'm not sure why you would want this. I would think that refinement is better done against the measured I, which may be slightly negative Phil On 24 Aug 2008, at 19:23, Ian Tickle wrote: Phil OK I admit I didn't delve very deeply into the code, but looking at the printer output it obviously does do a linear fit to the Wilson plot to get an overall B scale. However, looking at the man page (if all else fails read the documentation!) I see that it does say that this is only used to put the data on an approximately absolute scale. This is unnecessary of course - absolutely scaled data isn't needed for HA phasing MR, and the refinement will give a much more accurate scale factor anyway. Thanks for the info. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: 23 August 2008 08:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Wilson plot from truncated.mtz Actually Truncate ( ctruncate) do use a smoothed I in resolution shell (using a spline fit), not a linear Wilson plot Phil On 22 Aug 2008, at 20:30, Ian Tickle wrote: This indeed raises the question of whether the assumed Wilson distribution is valid, and it's another point I was in fact going to bring up. As presently constructed, Truncate fits a straight line to the Wilson plot (based on Imeas) in order to determine the overall scale B, but to avoid the problem that the low res data for a typical protein deviates markedly from the theoretical distribution, it uses resolution limits determined by the RSCALE option. According to the man page, the low resolution limit is by default set to 4 Ang if the high res limit is higher than 3.5 Ang. This usually means that the straight line fit is good for the high res data, but very poor for the low res data, but at least this means that the assumed distribution is valid at high res where most of the weak data (i.e. the data most affected by the Bayes correction) is located, but not valid for any weak data at low res (there will obviously be some). As you point out translational NCS invalidates these assumptions since the form of the distribution changes, but then probably only a few % of structures suffer from this type of NCS. A better way to deal with this would surely be to forget about the Wilson plot and simply determine the average I in resolution shells, with perhaps spline interpolation between the bin means (this is actually the 'k-curve' method for determining E's, attributed originally to Karle
Re: [ccp4bb] how to calculate the occupancy of two Mixed ligand binding modes at the single active site
SHELXL has been able to refine such occupancies (e.g. as p and 1-p for the two ligands, i.e. one extra parameter) for many years, and if I have understood correctly last week's version of phenix_refine can do so too. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 25 Aug 2008, conancao wrote: Dear all: In a 1.8A protein crystal structure,I find clear extra positive electron density suggesting 2 possible different orientations of the same ligand at a single active site.I identify those two orientations by mannually fitting 2 orientations and then refining them separately. Got a question though.Does anyone know which program could calculate the percentage of occupancy of two different orientations based on the mixture of electron density at the active site in the omit map. Or does any program could refine the the same ligand with 2 different orientations into a mixed electron density? Thanks a lot. Sincerely, Hongnan Cao Biochemistry Department UC Riverside _ 快来看看这些猫咪有多逗，爆笑！ http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AAForm=MEVHAA
Re: [ccp4bb] Wilson plot from truncated.mtz
Dear Ian and Phil, I am very reluctant to touch the experimental data, so I am a bit concerned about the argument that it is better to refine against F^2 than Imeas. Are you sure that the 'best estimate' of the intensity is also unbiassed? To take an extreme example, suppose that we have processed the data to a higher resolution than the crystal actually diffracts. The mean of Imeas in the outer shell should then be zero. The 'best estimate' of F^2 must however be slightly positive for all reflections, and recycling the estimation procedure will not change this. The affect on the refinement will be to reduce all B-values a little, i.e. it will lead to a biassed model. This is of course a purely theoretical discussion, there is no need for anyone to retract their published structures. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Sun, 24 Aug 2008, Ian Tickle wrote: Phil Squaring the F (i.e. the best estimate of Ftrue) that Truncate estimates does not give you F^2 (the best estimate of Itrue): F = Integral[0:infinity] sqrt(J) p(J|I) dJ var(F) = Integral[0:infinity] (sqrt(J)-F)^2 p(J|I) dJ F^2= Integral[0:infinity] J p(J|I) dJ var(F^2) = Integral[0:infinity] (J-F^2)^2 p(J|I) dJ where p(J|I) = p(I|J) p(J) / p(I) [Bayes Theorem] and I = Imeas, J = Itrue. From the eqn for var(F) we see that var(F) = F^2 - F^2, or F^2 = F^2 + var(F), i.e. F^2 is not the same as F^2. If you want to use the true F^2 in a calculation, isn't F^2 the best estimate by definition? Using Imeas in a calculation where Itrue is called for is exactly equivalent to assuming a uniform Bayesian prior p(J) on Itrue, i.e. you're assuming that all true values of I (constrained at least to be = 0 by physics and constrained further by the assumed distribution of atom positions) from -infinity to +infinity are equally likely!! - so you're throwing away all prior knowledge about the data. It doesn't seem logical to make use of prior info to estimate F but then not use it to estimate F^2. By using F^2 wouldn't you be making the best use of your prior knowledge? Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: 24 August 2008 20:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Wilson plot from truncated.mtz You're right. The smoothed I is used for the Truncate procedure, though it is difficult in the very low resolution bins. Also it doesn't allow for pseudo-translations, which it should. As you say, the linear fit is only used to put data on a very rough absolute scale. This isn't necessary, but it doesn't hurt There's no reason why truncate shouldn't give a best estimate of |F| ^2 but I'm not sure why you would want this. I would think that refinement is better done against the measured I, which may be slightly negative Phil On 24 Aug 2008, at 19:23, Ian Tickle wrote: Phil OK I admit I didn't delve very deeply into the code, but looking at the printer output it obviously does do a linear fit to the Wilson plot to get an overall B scale. However, looking at the man page (if all else fails read the documentation!) I see that it does say that this is only used to put the data on an approximately absolute scale. This is unnecessary of course - absolutely scaled data isn't needed for HA phasing MR, and the refinement will give a much more accurate scale factor anyway. Thanks for the info. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: 23 August 2008 08:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Wilson plot from truncated.mtz Actually Truncate ( ctruncate) do use a smoothed I in resolution shell (using a spline fit), not a linear Wilson plot Phil On 22 Aug 2008, at 20:30, Ian Tickle wrote: This indeed raises the question of whether the assumed Wilson distribution is valid, and it's another point I was in fact going to bring up. As presently constructed, Truncate fits a straight line to the Wilson plot (based on Imeas) in order to determine the overall scale B, but to avoid the problem that the low res data for a typical protein deviates markedly from the theoretical distribution, it uses resolution limits determined by the RSCALE option. According to the man page, the low resolution limit is by default set to 4 Ang if the high res limit is higher than 3.5 Ang. This usually means that the straight line fit is good for the high res data, but very poor for the low res data, but at least this
Re: [ccp4bb] CCP4i on MacPro under Leopard
Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] protein degradation
Hi Debajyoti, There is another simple thing you can try: Raise your NaCl concentration to 500 or 1000 mM in your lysis buffer. This helps to clean up your sample further and it might inhibit proteases in your lysate. Good luck, christian Debajyoti Dutta wrote: Hi, This is going to be an off topic question concerning this community. I have a protein 6XHis tagged. When retrieved from the Ni-NTA column with imidazole found to be degraded, appears like a deep band with other bands (touching each other below the main band) in SDS PAGE. The protein is a DNA binding (pI~ 10) and Tris-Hcl buffer is used with 10% glycerol and 300mM NaCl. for purification. Does Phosphate buffer do any help in stopping the degradation. All suggestions are welcome. Thank you for your reply in advance. Sincerely Debajyoti Dutta Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3OAS_QUERY=null ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
[ccp4bb] TLS refinement
Hello, I have a question about comparing anisotropic displacement parameters for a series of 6 mutant and a wt structure with diffraction from 1.2-1.5 Å. The space group and unit cell for the series is the same, and most xtals were obtained by seeding from a hit for one mutant. There are two mols in the ASU which form an NCS dimer and the mutations alter dimer contacts in the xtals, and also alter dimer Kd measured by AUC. However, some of the mutants do not measurably dimerize in solution, but still form dimers in the xtal lattice. When I study the individual anisotropic displacement parameters (derived from decomposition of the TLS tensors using TLSANL) of the structural elements making up the dimer interface, the magnitude and anisotropy of the displacements are increased for the complexes that form weaker dimers or dont dimerize at all in solution. I interpret this as a reflection of the weakened or non-existent interaction between monomers observed in solution for these complexes. But the question is how valid is it really to compare across-crystals? The total anisotropic displacement parameter U(tot) = U(cryst) + U(int) + U(atom) +U(TLS) so presumably cross-crystal differences are being accounted for by the single anisotropic parameter applied to the unit cell in Ucryst which would suggest that drawing such conclusions across crystals may be reasonable. Any insights or thoughts would be greatly appreciated. Thanks very much, Charu
Re: [ccp4bb] CCP4i on MacPro under Leopard
Thanks a lot for this hint: it works! Including REFMAC, which ran to completion and used Arp/Warp to add waters successfully. Anita Le 25 août 08 à 16:04, William G. Scott a écrit : Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] calculate occupancy for 2 different ligand binding modes at the same active site
Thanks Herman, George and Leo.I will try the methods.Their suggestions are summarized below. Dear Hongnan-- On 25 Aug 2008, at 17:47, conancao wrote:Or does any program could refine the the same ligand with 2 different orientations into a mixed electron density? That's an easy onehttp://scripts.iucr.org/cgi-bin/paper?ba5073http://cns-online.org/v1.21/ (see the alternate.inp file)http://www.phenix-online.org/documentation/refinement.htm#anch323 (see the infos on conformation) HTH Kind regards. -- Leo -- SHELXL has been able to refine such occupancies (e.g. as p and 1-p for the two ligands, i.e. one extra parameter) for many years, and if I have understood correctly last week's version of phenix_refine can do so too. George Dear Hongnan,What I usually do is to calculate an omitmap and calculate the electron density value(s) of (an) atom(s) which do not overlap and convert that to relative occupancies. The sum can of course not be more then one and all atoms of each molecule have the same occupancy. I use my own program to calculate the electron density value at atomimic positions, but I am pretty sure the CCP4 or phenix or so will also have programs to do this. An even easier alternative might be to scroll in coot the electron density up and down and note point where the density just disappears for the atom(s) in question. From my experience, there is no need to determine the occupancies with more accuracy then 10%, e.g. occupancies like 0.1, 0.2, 0.3 etc. since they are linked to the B-factors anyways at this resolution. Best regards,Herman _ 看MSN史诗巨片，票选人气角色，赢取PSP等诸多好礼！ http://im.msn.cn/
Re: [ccp4bb] Wilson plot from truncated.mtz
George Phil - Having slept on this it's beginning to dawn on me that George is right and my assertion that F^2 is the appropriate data to use in MR and F^2-based refinement was incorrect. However my assertion that F^2 is the best estimate of F^2 (and that F is the best estimate of F) is still valid. It took me a while to realise how these statements could be reconciled, but the basic point is that the relevant prior to use in Bayesian inference depends on what you are trying to infer (kind of obvious really!). So if the goal of the X-ray experiment is to infer the most accurate estimates of the individual amplitudes or intensities, the relevant prior is that of the amplitude or intensity respectively. Similarly if the goal is to infer the true average intensity (which can never be exactly zero), the relevant prior to use is that of the average intensity. This should give the right answer, which will be different from the (wrong) answer obtained by using the individual intensity priors and averaging the best estimates of the intensities. Similarly you don't get the best estimate of F^2 by squaring the best estimate of F obtained from the F prior: you have to use the F^2 prior to get F^2 directly. If the goal is to get the electron density map, the electron density prior is the appropriate one to use (this prior will obviously require that the amplitudes of the FT of the density are real numbers). Since the purpose of the X-ray experiment is (usually) to obtain the best estimates of the atomic or group parameters x,y,z,B (or Uaniso, TLS etc), the relevant priors to use are those of the atomic or group parameters and the amplitude/intensity priors don't (or shouldn't) come into it. It seems to me that this implies that the procedure we are using to first estimate F using the F prior and then use F in refinement is fundamentally flawed: it's really only a hack to get around historical deficiencies in the software. The formally correct procedure would seem to be to use Imeas directly in the refinement, and then of course the F^2 prior doesn't come into it (since the goal of refinement is not to estimate F^2). I realise that this is something that George has been advocating for a long time! Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick Sent: 25 August 2008 10:37 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Wilson plot from truncated.mtz Dear Ian and Phil, I am very reluctant to touch the experimental data, so I am a bit concerned about the argument that it is better to refine against F^2 than Imeas. Are you sure that the 'best estimate' of the intensity is also unbiassed? To take an extreme example, suppose that we have processed the data to a higher resolution than the crystal actually diffracts. The mean of Imeas in the outer shell should then be zero. The 'best estimate' of F^2 must however be slightly positive for all reflections, and recycling the estimation procedure will not change this. The affect on the refinement will be to reduce all B-values a little, i.e. it will lead to a biassed model. This is of course a purely theoretical discussion, there is no need for anyone to retract their published structures. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Sun, 24 Aug 2008, Ian Tickle wrote: Phil Squaring the F (i.e. the best estimate of Ftrue) that Truncate estimates does not give you F^2 (the best estimate of Itrue): F = Integral[0:infinity] sqrt(J) p(J|I) dJ var(F) = Integral[0:infinity] (sqrt(J)-F)^2 p(J|I) dJ F^2= Integral[0:infinity] J p(J|I) dJ var(F^2) = Integral[0:infinity] (J-F^2)^2 p(J|I) dJ where p(J|I) = p(I|J) p(J) / p(I) [Bayes Theorem] and I = Imeas, J = Itrue. From the eqn for var(F) we see that var(F) = F^2 - F^2, or F^2 = F^2 + var(F), i.e. F^2 is not the same as F^2. If you want to use the true F^2 in a calculation, isn't F^2 the best estimate by definition? Using Imeas in a calculation where Itrue is called for is exactly equivalent to assuming a uniform Bayesian prior p(J) on Itrue, i.e. you're assuming that all true values of I (constrained at least to be = 0 by physics and constrained further by the assumed distribution of atom positions) from -infinity to +infinity are equally likely!! - so you're throwing away all prior knowledge about the data. It doesn't seem logical to make use of prior info to estimate F but then not use it to estimate F^2. By using F^2 wouldn't you be making the best use of your prior knowledge? Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: 24
[ccp4bb] Postdoctoral Position (Structural Biology of the Actin Cytoskeleton, University of Pennsylvania School of Medicine)
A postdoctoral position is available immediately to study the structure and function of actin cytoskeleton dynamics. The actin cytoskeleton is a vast area, involving actin-binding proteins, signaling proteins, cytoskeleton scaffolding and membrane binding proteins. Most of the projects deal with protein complexes and involve large-scale protein expression and purification, biochemical and biophysical characterization and protein crystallography. Potential candidates should have a recent Ph.D. in biochemistry or biophysics. We offer competitive salary and benefits and outstanding opportunities for career development. Lab Web Page: http://www.med.upenn.edu/dominguez/ Contact: Roberto Dominguez, Ph.D. Associate Professor of Physiology University of Pennsylvania School of Medicine A507 Richards Bldg 3700 Hamilton Walk Philadelphia, PA 19104-6085 Telephone: 215-573-4559 Fax: 215-573-5851 E-mail: [EMAIL PROTECTED]
[ccp4bb] Air Conditioning System for Optical Hutch
Hello Everyone!... I'm starting to thing about an air conditioning system for the optical hutch of one of our beamlines, which suffers from positional and energy drifts associated with several sources. It's clear that the specifications for such system can cover a wide range of requirements. However at the present time I would like to just have a feeling of how much I would probably spend with a system like that. Someone who already had to commissioning one could give some idea? I hope you are all fine, Lucas Sanfelici Physicist Brazilian Synchrotron Ligth Source- LNLS ( http://www.lnls.br www.lnls.br) Diagnostics Group PO Box 6192 Postal Code 13083-970 Campinas-SP Brazil Phone: +55-19-3512-1153/1152 Fax: +55-19-3512-1006 E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] CCP4i on MacPro under Leopard
Glad it worked. I should have written sudo /bin/bash or sudo /bin/zsh or sudo /bin/tcsh followed by sourcing the appropriate startup script. However, if I run the tcsh command, I get this error: limit: stacksize: Can't remove limit (Invalid argument) oddly, this does not happen with a non-root version of tcsh. It is easier I think just to use /bin/bash or /bin/zsh in this case. On Aug 25, 2008, at 9:09 AM, Anita Bentley wrote: Thanks a lot for this hint: it works! Including REFMAC, which ran to completion and used Arp/Warp to add waters successfully. Anita Le 25 août 08 à 16:04, William G. Scott a écrit : Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
[ccp4bb] Problems installing MOSFLM on Leopard
Hi there! Real noobie question here- I am hoping someone can help me. I have been trying to download and install MOSFLM from the pre-built versions here: http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703/pre-built/index.html Specifically, I am trying to install the Universal version for OSX (although I have also tried the OSX 10.4 version for Intel). It downloads as a document, and unzips just fine. But it refuses to run- I get an error: There is no default application specified to open the document mosflm_osx_10.4_intel for that version. For the Universal version, nothing happens- I double click the unzipped file, and nothing happens. I've also tried Fink, and I get a bunch of stuff that ends in: ./build * CCP4 appears to have been set up properly - checking libraries You must install CCP4 version 5 (or later) - Mosflm no longer builds with CCP4 version 4 or earlier. cd bin mv ipmosflm ipmosflm-701 mv: rename ipmosflm to ipmosflm-701: No such file or directory ### execution of /var/tmp/tmp.1.pRoow1 failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-mosflm-7.0.1-2 (Reading database ... 19861 files and directories currently installed.) Removing fink-buildlock-mosflm-7.0.1-2 ... Failed: phase compiling: mosflm-7.0.1-2 failed I'm running Leopard on a MacBook with plenty of RAM. Any suggestions as to what to try? -T
[ccp4bb] Position announcement
A postdoctoral position is available to continue our study on the crystal structures of blood coagulation proteins, particularly Factor VIII (Structure. 2008;16:597-606). This is the protein missing in hemophilia. The candidate should have a sound knowledge and experience in protein X-ray crystallography and protein biochemistry. The work will include preparation of protein-protein complexes, biological assay, crystallization, and structure determination. This laboratory is a satellite of the Center for Hemostasis and Thrombosis located in the Harvard Medical School complex in Boston. Funds are available to support this position for up to three years. The most successful candidate will have an opportunity to develop an independent career via this laboratory at the MBL. The successful candidate must have a PhD degree in a relevant field and previous research experience in protein X-ray crystallography. Protein chemistry skills will be important for this position. The position would suit a highly motivated and energetic individual who is keen to work in a multidisciplinary environment involved in structural biology research. Independence and ability to solve experimental problems are critical. Interested persons should send a detailed CV, covering letter and contact details of three referees to Bruce Furie at [EMAIL PROTECTED] (please do not reply to this sender).
