Re: [ccp4bb] atomic FF used in SFALL
I wrote that - is a constant a Gaussian? Anyway that is how I got 5 - and it is the 9-parameter Cromer-Mann approximation.. And Yes - each component is added to the B value to build up the real space atomic density. as you show. Eleanor Bernhard Rupp wrote: Dear All, I read in SFALL docu that a 2- or 5-Gaussian approximation for SFs is used - I quote from SFALL docu: begin a1*exp(-b1*s*s) + a2*exp(-b2*s*s) - 2 Gaussian approximation (Agarwal, 1978) or as: a1*exp(-b1*s*s) + a2*exp(-b2*s*s) + a3*exp(-b3*s*s) + a4*exp(-b4*s*s) + c - 5 Gaussian approximation ---end Note: 1) The second formula is a 4, not 5 Gaussian approximation - Is it the 9-parameter Cromer-Mann approximation? 2) If so, one would need to convert this (reciprocal space) scattering function into real space e-density when making the map to be FFTed: rho(r) - FT - f(s) -this f(s) is what the scattering formula above describes for example from recip: exp(-Bs*s/4) I would get FT-1 - real: ((4pi/B)**3/2)exp(-4pi**2*r**2/B) and use that actually to decribe the atom shape in the map generation. True? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - Every day above ground is a good day. -
Re: [ccp4bb] atomic FF used in SFALL
In any case it will become a Gaussian because presumably the atomic B's are added to the b terms for the density calculation? -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: 11 October 2007 09:26 To: [EMAIL PROTECTED] Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] atomic FF used in SFALL I wrote that - is a constant a Gaussian? Anyway that is how I got 5 - and it is the 9-parameter Cromer-Mann approximation.. And Yes - each component is added to the B value to build up the real space atomic density. as you show. Eleanor Bernhard Rupp wrote: Dear All, I read in SFALL docu that a 2- or 5-Gaussian approximation for SFs is used - I quote from SFALL docu: begin a1*exp(-b1*s*s) + a2*exp(-b2*s*s) - 2 Gaussian approximation (Agarwal, 1978) or as: a1*exp(-b1*s*s) + a2*exp(-b2*s*s) + a3*exp(-b3*s*s) + a4*exp(-b4*s*s) + c - 5 Gaussian approximation ---end Note: 1) The second formula is a 4, not 5 Gaussian approximation - Is it the 9-parameter Cromer-Mann approximation? 2) If so, one would need to convert this (reciprocal space) scattering function into real space e-density when making the map to be FFTed: rho(r) - FT - f(s) -this f(s) is what the scattering formula above describes for example from recip: exp(-Bs*s/4) I would get FT-1 - real: ((4pi/B)**3/2)exp(-4pi**2*r**2/B) and use that actually to decribe the atom shape in the map generation. True? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - Every day above ground is a good day. - Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Refmac and planar amide restraint
Dear Jason, you will have to include the planarity either by introducing torsion restraints for the specified bonds, or by using the plane definition. Pls. be aware that in the current refmac versions the plane definitions will be used with a fixed sigma, i.e. the value of the dictionary is not used. For the torsion restraints you will have to include them explicitly in the input, check the earlier posting on torsion restraints. Garib kindly made an experimental version of refmac which allows easier inclusion of torsions from the dictionary AND the inclusion of the sigmas for the plane definitions (One sigma for each plane group, taken from the first atom in the group in the dictionary). see for linux binaries: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_linintel.tar http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html Hope that helps, Eckhard Jason Greenwald schrieb: Dear all, How does one tell Refmac that the bond between two non-amino-acid monomers should be planar (in the case that this bond is an amide)? My ligand has amino-acid and non-animo-acid constituents that are connected via amides. I have made library definitions for all of the non-standard parts and Refmac accepts these and makes the bonds between the various monomers in the ligand but treats them as single bonds and therefore fully rotatable. Cheers. Jason -- Eckhard Hofmann [EMAIL PROTECTED] Ruhr-Uni Bochum AG Proteinkristallographie, LS Biophysik, ND04/316 44780 Bochum Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
[ccp4bb] Refmac and planar amide restraint
Dear all, How does one tell Refmac that the bond between two non-amino-acid monomers should be planar (in the case that this bond is an amide)? My ligand has amino-acid and non-animo-acid constituents that are connected via amides. I have made library definitions for all of the non-standard parts and Refmac accepts these and makes the bonds between the various monomers in the ligand but treats them as single bonds and therefore fully rotatable. Cheers. Jason
[ccp4bb] PhD student position at the Max-Delbrueck Center in Berlin
We are looking for a PhD student with Master’s degree to explore structure and function of G-Proteins and their interaction with membranes. The project will include X-ray crystallographic studies and biochemical experiments including liposome binding and deformation studies by electron microscopy, nucleotide binding and hydrolysis assays, and also some cell biology - have a look at our recent publications for the research we are interested in. We are located at the Max-Delbrueck Center in north of Berlin (Helmholtz institute) and are well equipped with two FPLC and one HPLC system, large scale bacteria shakers, two X-ray rotating anode with MAR imaging plates, two pipetting robots and an extensive crystal imaging system. Furthermore, synchrotron radiation is available in close proximity at BESSY in the south of Berlin. For further information please contact me ([EMAIL PROTECTED] mailto:[EMAIL PROTECTED]), or send me your application including CV and addresses of two possible referees. Thanks a lot, Oliver Daumke Crystallography group Max-Delbrueck Centre for Molecular Medicine Robert-Roessle-Strasse 10 10435 Berlin Daumke O., Lundmark R., Vallis Y., Martens S., Butler P.J., McMahon H.M. (2007) Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling. *Nature*, DOI: 10.1038/nature06173 Daumke, O., Weyand , M., Chakrabarti P.P., Vetter I., Wittinghofer A. (2004) The GTPase‑activating protein Rap1GAP uses a catalytic asparagine. *Nature* 429, 197-201
[ccp4bb] b-factor sharpening and FFT/CAD
Hi all, I know this was most addressed by Eleanor back on June 14, 2007... and I've had no problems making such sharpened maps. But I'm confused as to why FFT decides to put SCALE 2.0 -100.0 in the command file by default, and not SCALE 1.0 -100.0; I've been correcting this manually. Any thoughts? Thanks, Roni
Re: [ccp4bb] His tag does not bind.
We have found that our His-MBP fusion doesn¹t bind well after we cut off the protein of interest, and are trying to remove it. We have to use very low salt, cold temp, and slow loading rates. You might also try batch instead of column loading. We have also had good luck adding 1-2M urea to uncut His-MBP-protein fusions that show poor binding to the Qiagen Ni-NTA. Kendall On 10/10/07 9:12 PM, changrui lu [EMAIL PROTECTED] wrote: Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his-column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance. Ray Cornell Univerisity
Re: [ccp4bb] His tag does not bind.
150Kd is a fairly large protein for a MBP (55Kd) fusion. Six His-tag may not strong enough for it to bind to the Ni-column. If protein overexpression and solubility is not an issue, I would avoid using MBP fusion. Depend on how your protein fold, sometimes N-terminal His-tag works, sometimes C-terminal. If your N-terminal protein hide inside of the tertiary structure, try to clone it into a C-terminal His-tag vector. pET vectors offer easy switch. Good luck. Helen RD/ABI From: Kendall Nettles [EMAIL PROTECTED]Reply-To: Kendall Nettles [EMAIL PROTECTED]To: CCP4BB@JISCMAIL.AC.UKSubject: Re: [ccp4bb] His tag does not bind.Date: Thu, 11 Oct 2007 11:34:46 -0400 We have found that our His-MBP fusion doesnt bind well after we cut off the protein of interest, and are trying to remove it. We have to use very low salt, cold temp, and slow loading rates. You might also try batch instead of column loading. We have also had good luck adding 1-2M urea to uncut His-MBP-protein fusions that show poor binding to the Qiagen Ni-NTA. KendallOn 10/10/07 9:12 PM, "changrui lu" [EMAIL PROTECTED] wrote: Dear all,I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his-column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance.RayCornell Univerisity Make every IM count. Download Messenger and join the im Initiative now. Its free.
Re: [ccp4bb] His tag does not bind.
Recently, a make-or-break difference for me was making sure the pH was what I thought it was: In the presence of 50mM HEPES pH 7.0 (at room temp), the pH of my protein sample was actually nearer to 6 at 4degC, as judged by pH paper. I am not sure whether the pH difference was mainly because of the temperature drop or because of other components in the mixture, but adding an additional 50mM TRIS pH 8.5 (RT) made all the difference. The pH paper after this addition indicated a pH of 7-8. In the former case, the protein was completely undetectable in elution fractions, and in the latter, was successfully purified. Of course this makes complete biochemical sense, but nevertheless I am very glad I checked the pH. Jacob Keller On Wed, 10 Oct 2007 8:12:46 pm CDT changrui lu wrote: Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his-column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance. Ray Cornell Univerisity ===End of original message text=== *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***
Re: [ccp4bb] His tag does not bind.
Try batch binding. Sometimes batch binding for 30 min is more efficient than column binding. If your protein binds DNA, treat with DNase or Benzonase. Adding detergent may help as has been suggested. --Chun _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of changrui lu Sent: Wednesday, October 10, 2007 6:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] His tag does not bind. Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his-column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance. Ray Cornell Univerisity
Re: [ccp4bb] His tag does not bind.
Many brands of pH paper give 0.5-1 pH reading lower for Hepes buffer. pH meter is more reliable to measure the pH of Hepes buffers. Tris pH increases in cold. If TCEP is used as reducing agent, make sure the stock solution has been pH-adjusted. --Chun -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: Thursday, October 11, 2007 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] His tag does not bind. Recently, a make-or-break difference for me was making sure the pH was what I thought it was: In the presence of 50mM HEPES pH 7.0 (at room temp), the pH of my protein sample was actually nearer to 6 at 4degC, as judged by pH paper. I am not sure whether the pH difference was mainly because of the temperature drop or because of other components in the mixture, but adding an additional 50mM TRIS pH 8.5 (RT) made all the difference. The pH paper after this addition indicated a pH of 7-8. In the former case, the protein was completely undetectable in elution fractions, and in the latter, was successfully purified. Of course this makes complete biochemical sense, but nevertheless I am very glad I checked the pH. Jacob Keller On Wed, 10 Oct 2007 8:12:46 pm CDT changrui lu wrote: Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his-column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance. Ray Cornell Univerisity ===End of original message text=== *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***
Re: [ccp4bb] His tag does not bind.
Let me make three short notes: 1. If the protein does not bind in a 'normal' buffer try first under denaturing conditions to see if everything is expressed correctly (a repeat of Artem's suggestion basically!). Protocols for that are in all materials manuals. 150 kD in E.coli is very very tough. 190 is even tougher. If you use a C-term tag, which has also the advantage it will select 'full length' proteins, take care of the first few codons; His- and other Tags are optimized for that. A silent mutation at position 4-5 (after the ATG) has made for us an easy 10-20 fold difference in the past. 2. Most buffer change pH depending on temperature. See for example: http://www.neb.com/nebecomm/tech_reference/general_data/tris_buffer.asp Always measure pH at the temperature you plan to work at, or make sure you always measure at the same temperature and be aware of the problem, look-up tables as above exist for many buffers. 3. For such a long protein an optimized-codon synthetic gene worked really well for us for a 100 kD protein, boosting expression 10-fold. consider it if it ends up to be low- yield trouble. A. On 11 Oct 2007, at 19:02, Jacob Keller wrote: Recently, a make-or-break difference for me was making sure the pH was what I thought it was: In the presence of 50mM HEPES pH 7.0 (at room temp), the pH of my protein sample was actually nearer to 6 at 4degC, as judged by pH paper. I am not sure whether the pH difference was mainly because of the temperature drop or because of other components in the mixture, but adding an additional 50mM TRIS pH 8.5 (RT) made all the difference. The pH paper after this addition indicated a pH of 7-8. In the former case, the protein was completely undetectable in elution fractions, and in the latter, was successfully purified. Of course this makes complete biochemical sense, but nevertheless I am very glad I checked the pH. Jacob Keller On Wed, 10 Oct 2007 8:12:46 pm CDT changrui lu wrote: Dear all, I am trying to express a 150 kd protein in E coli. I have it in two constructs, one with pmal-his and other with only his tag at N terminus. The full length protein can be detected both by sds and western using anti-his (190kd and 150kd respectively) but strangely neither binds to his- column very well. The majority of the full length comes through the column either at loading step or low salt wash step. The major species that gets trapped and eluted is the mbp-his truncation (~40kd). Some, though very little, full length protein did make it out the his column. The pmal-his construct does not bind amylose resin any better with majority flows right through. All purification are carried out under standard conditions as mentioned in the manuals. The protein is soluble and does not precipitate in the columns. I appreciate and ideas or explanations. Thanks in advance. Ray Cornell Univerisity ===End of original message text=== *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***
Re: [ccp4bb] atomic FF used in SFALL
what is the limit of N in a practical case for the Gaussian approximation. The resolution. Less resolution, less terms needed. see Acta papers TenEyck 1977 particularly Agarwal 1978, and the cctbx section in newsletter: http:// http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf br _ From: Jayashankar [mailto:[EMAIL PROTECTED] Sent: Thursday, October 11, 2007 10:54 AM To: [EMAIL PROTECTED] Subject: Re: [ccp4bb] atomic FF used in SFALL On 10/11/07, Bernhard Rupp mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] wrote: It seems that 5-Gaussian is indeed the accepted technical term for the 9-parameter expansion: Given that a5=c and b5=0, the 5th Gaussian can be a constant. Continuing this reasoning, even a binary mumber can be represented as series of Gaussians.a=0,b=0; a=1, b=0 This is called 'Gomputing'. Cheers, br -Original Message- From: Eleanor Dodson [mailto:[EMAIL PROTECTED] Sent: Thursday, October 11, 2007 1:26 AM To: [EMAIL PROTECTED] Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] atomic FF used in SFALL I wrote that - is a constant a Gaussian? Anyway that is how I got 5 - and it is the 9-parameter Cromer-Mann approximation.. And Yes - each component is added to the B value to build up the real space atomic density. as you show. Eleanor -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
[ccp4bb] PhD student position available
This email is sent on behalf of Prof. Stefan Szedlacsek in the Institute of Biochemistry of the Romanian Academy of Sciences in Bucharest. Application for PhD Programme in Structural biology and enzyme kinetics Applications are welcomed for a PhD student position in the Department of Enzymology of the Institute of Biochemistry of the Romanian Academy of Sciences in Bucharest (Romania). This position is funded under a new FP6 Marie Curie Research Training Network - PTPNET. The Network contains twelve research teams and will focus in depth on protein tyrosine phosphatase (PTP) structure, regulation and function. This Network will be highly collaborative in nature, providing exciting opportunities for researchers to work in several disciplines and to be exposed to both academia and industry. The team leader of the Romanian group is Professor Stefan Szedlacsek. The specific interest of the group is to understand the structure-function relationships of PTPs and their possible relevance for the physiological functions of PTPs. Using an enzyme kinetic approach, this group has so far obtained important results concerning the interrelationship between intracellular regions of PTPmu. In addition, the group crystallized and solved (in a highly successful international collaboration) the corresponding crystal structure of PTP-SL/BR7; the first structure of a receptor-like PTP with a single cytoplasmic domain. Given the the unique expertise of the group in enzymatic analysis (particularly enzyme kinetics), as well as their structural biology experience the group provides the main Network expertise in enzyme kinetics, screening facilities for substrate specificity analysis as well as tools for structural analysis of the extracellular regions of PTPs. Two main goals are set for this PhD project. First: to determine the 3D-crystal structure of non-catalytic cytoplasmic subdomains of PTPs. Second: to evaluate the substrate specificities and determine the effects of specific modulators and mutations on the enzymatic activity of PTPs. It is also intended to perform correlation analysis between structural and activity data thus obtained. Modern experimental procedures will be applied, like recombinant DNA technologies, protein expression, protein purification and crystallization, spectroscopy, enzyme kinetics analysis. The successful PhD student will be given intensive Network training through dedicated workshops and will be given opportunities to work with other teams during secondments. For further details please e-mail: [EMAIL PROTECTED]
[ccp4bb] SFALL grid
Hi: I am trying to generate structure factors from a mask/map that I made with NCSMASK. I get the following error message in SFALL: The program run with command: sfall HKLOUT /tmp/whittle/109_5_7_1_mtz.tmp MAPIN /home/whittle/projects/109_5/CCP4/center_50.msk has failed with error message SFALL: Grid too small- NZ must be 2*Lmax+1 Which grid is this referring to? The grid used by SFALL or by NCSMASK when I initially generated the map? How does one choose an appropriate grid and extent for these programs? Thanks for your help! --James
Re: [ccp4bb] SFALL grid
SFALL is calculating structure factors from the map you supplied, so there is only one grid, the one you used when you created the map in NCSMASK. The choice of sampling rates for maps to be Fourier transformed is a deep topic. The mathematical law is that you have to sample the map at, at least, twice the frequency of the highest Fourier component in the map. This is, unfortunately, often misinterpreted as twice the frequency of the highest component you are interested in. The fact that you are interested in, say, 2A structure factors has nothing to do with the calculation of the Fourier transform of your map. All that matters is the frequencies that were present in your map before you sampled it on the grid. Ten Eyck, (1977) Acta Cryst A33, 800-804 has a discussion of this and provided the classic solution to this problem when the map to be transformed is a calculated electron density map. I presume you have an NCS averaged map and the required interpolations introduce needs of their own that are significant. Gerard Bricogne has written on that topic, also back in the 1970's, but I don't have the reference at hand. The manual for your NCS averaging program should give you guidance on the choice of sampling rate based on its interpolation method. If you are not even sampling at twice the resolution you are interested in you are sampling way too coarsely. All FFT based structure factor programs require that the sampling rates along each axis be even. They may have other required factors depending on the space group, but they will be happy to inform you if you make a choice it doesn't like. They are also more efficient when the prime factors of the sampling rates are small numbers. Try to stick with multiples of 2,3, and 5 if possible. Since the program has no way of knowing the highest resolution component actually in the map before you sampled it on your grid, it assumes that the map contains no components of higher resolution then you asked it to produce. All FFT programs will fail if you sample your map courser than twice that frequency, as SFALL did for you. That does NOT mean that twice the frequency you are interested in is sufficient. You MUST read your NCS averaging program's documentation and if that doesn't tell you, complain the the program's author, and read Gerard's papers on the matter. NCS averaging a map that is only sampled at twice the rate you are interested in will not be a useful way to spend your time. Dale Tronrud whittle wrote: Hi: I am trying to generate structure factors from a mask/map that I made with NCSMASK. I get the following error message in SFALL: The program run with command: sfall HKLOUT /tmp/whittle/109_5_7_1_mtz.tmp MAPIN /home/whittle/projects/109_5/CCP4/center_50.msk has failed with error message SFALL: Grid too small- NZ must be 2*Lmax+1 Which grid is this referring to? The grid used by SFALL or by NCSMASK when I initially generated the map? How does one choose an appropriate grid and extent for these programs? Thanks for your help! --James
