[ccp4bb] sunrider
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Re: [ccp4bb] Micocrystals or not?
Dear All, Thank you for all your replies, I think there are some additional informations about this screening to help judgment: 1. this screening was set in a 0.2+0.2 microliter drop, so the microcrystals(?) are very small. 2. these things came out in different conditions, after 1-4 days, and didnot grow bigger. 3. the protein buffer contains 500mM NaCl while most of the screen conditions has ethanol, so could them be NaCl crystals? One more question: has anybody experienced that the N-terminal histag cannot be cut off, but it is really there and helps the purification? Is any information can be achieved from this? Thanks a lot! Best Yang On Mon, Sep 20, 2010 at 6:28 PM, yang li robertcatru...@gmail.com wrote: Dear All, After crystal screening I got something look like microcrystals but not sure, picture taken by the robot is attached. I am new in protein crystallization, I wonder if anybody can give me a guidance about this situation, and how to optimize the condition if they are real protein crystals. Any suggestion will be appreciated! Best Yang
[ccp4bb] How to optimize protein-DNA complex conditions?
Dear All, Recently I am working on a protein-DNA complex, and from running agarose gel, there is a weak delayed band after the band of pure DNA which indicates some DNA has bind to the protein though the binding efficiency is low. Then I tried to optimize the condition to increase the binding, but it did not work since the intensity of the delayed band didnot grow. The condition I used is list below: 1. the concentration of protein is about 1.5mg/ml, buffer in Tris-Cl, PH 8 and NaCl. 2. the running buffer for agarose gel is 0.5x TBE, PH 8.3. 3. different ratio of protein: DNA has tried, from 2:1 to 1:2. 4. different concentration of NaCl, MgCl2 and ATP in reaction system have been added, but no significant change. I wonder if there is any way to increase the binding efficiency? Is it possible to set up crystal plates in this situation, with protein and complex together? Any suggestion would be appreciated! Best Yang
[ccp4bb] Off topic: PKa of protein-DNA complex.
Hi, Is there any server or program can calculate the theoretic PKa of the protein-DNA complex? Given the structure of the protein and the sequence of the DNA. Any suggestion will be appreciated! Best Yang
[ccp4bb] Merohedral twining for P212121.
Dear all, Is there any possible of twining for a normal P212121 spacegroup and what is the twin law, say no equal cell dimensions? Some people said there is no twin law for such symmetry but I am not very sure. Thanks a lot. Best Yang
Re: [ccp4bb] MR on low resolution soaking data.
Dear All, Thank you for your help! There do have something needed to be checked carefully, as you suggested. Peter Zwart showed me the right way of explore_symmetry_metric, which indicated there is some relationship between the two unit cells. I hope it can explain the strange wilsonB and failure of MR. I will try to reprocess the data later to make sure. Best wishes Yang On Tue, Jun 8, 2010 at 1:57 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: The easy Q first: Wilson plot B values are very unreliable for 4A data - b=20 is almost certainly wrong, but until you have a model to refine it is hard to get a proper estimate. Q2: With a decent model the ligand should show up as a blob, even at this resolution. You might have trouble fitting it, but at least you would know whether it had bound or not. Q3: Why the MR doesnt work - I cant answer this.. Check the data for any serious problems - missing strong intensities can mislead. Is the spce group certain? Is there any relationship between the P212121 and F222 cells? Eleanor w it ang li wrote: Dear colleagues, We are now trying to soak some ligands into a protein, which is about 60kd in size and the structure has been solved before. But the molecular replacement cannot give a right solution. Below is some contrast of the data: Native 2A P212121 monomer Soaked4A F222 monomer (more than 70% solvent) or dimer(more possible) I wonder if it is possible to find the ligand in the case of such low resolution, provided the ligand is not so small. What facts could probably lead to the failure of MR? Molrep gave a model of monomer but the rfree is as high as 0.7, while phaser could get no result. I tried phenix.explore_metric_symmetry to find the two spacegroups are not compatible, and the Rmerge of the data seems reasonable. One more question is: the wilson B of the data is lower than 20 from ccp4. Is it common for a 4A data? Since I donnot have the experience of handling this low resolution data yet. By the way, any suggestions about refinement methods in low resolution will be appreciated! Best wishes Yang
[ccp4bb] MR on low resolution soaking data.
Dear colleagues, We are now trying to soak some ligands into a protein, which is about 60kd in size and the structure has been solved before. But the molecular replacement cannot give a right solution. Below is some contrast of the data: Native 2A P212121 monomer Soaked4A F222 monomer (more than 70% solvent) or dimer(more possible) I wonder if it is possible to find the ligand in the case of such low resolution, provided the ligand is not so small. What facts could probably lead to the failure of MR? Molrep gave a model of monomer but the rfree is as high as 0.7, while phaser could get no result. I tried phenix.explore_metric_symmetry to find the two spacegroups are not compatible, and the Rmerge of the data seems reasonable. One more question is: the wilson B of the data is lower than 20 from ccp4. Is it common for a 4A data? Since I donnot have the experience of handling this low resolution data yet. By the way, any suggestions about refinement methods in low resolution will be appreciated! Best wishes Yang
[ccp4bb] Deal with close heavy atom sites?
Dear all, I have a 1.6A data in P21 spacegroup whith good quality, wich is assumed to contain 4 Set-Met. But the patterson map appears strange. There is a very big heavy peak in the harker section, and seems like an irregular ellipse, while there are small peaks very near(almost connect) to this big peak and the origin, say about 0.05 in fraction, looks like cross peaks.It looks like the heavy atoms are very close if there are more than one. I tried several programs and many heavy atom coordinates sits, but none of them can solve it. Shelxd got a set of sites looks best with set the minimum distance to 1A, since the patterson map from it looks like the experimental patterson map, though not very much. But with this HA sites can get nothing meaningful. By the way, it is a small molecule with no more than 150 residues, one molecule/ASU. According to shelxc the signal is not strong, can only be used to aroud 2.2A. Any suggestions would be appreciated!
[ccp4bb] Generate high resolution pirctures in pymol
Hi all, Can somebody please help me to generate high resolution movie files for secondary structure of proteins? After I ray a model with high resolution in pymol and then save it as movie frames, the high resolution and ray seem lost. I have tried the command likes ray 2000,2000 and it does work for a single frame, but can anybody tell me how it could be extended to say 40 or 80 frames of a movie? Your suggestions are highly appreciated. Thanks in advance!
Re: [ccp4bb] Refinement of anisotropic data
Hi, All, Thanks for all your replies. I checked the server as Pavel said, and found that the 2.3A data has strong anisotropy and other two has severe anisotropy. The recommend resolution cutoff in the c axis is only 3.4A. I need to read more about the manual but I think this is the problem. Hope this works. Thanks again!
[ccp4bb] Refinement of anisotropic data
Hi, I have a structure with 3 different resolutions, 2.3A, 2.4A, 2.5A, the qualities seem normal, not good but also not too bad. The B factors along a,b,c axis have notable difference, for example B(a)=80, B(b)=30, B(c)=20. We used molecular replacement to solve the structure. For the 2.3A data, the final Rfree is 0.265 from phenix.refine without tls since tls will increase the Rfree much. But for the 2.4A data, the Rfree wonnot low down to 0.32, though the map seems not bad(with only a few solvent atoms). And for the 2.5A data the Rfree is even higher than 0.4. For all of them I used thinshell and followed the same procedure: MR--rigid body refinement--restrain refinement--phenix.autobuild--manually check--phenix.refine(ordered solvent) And autobuild can always build more than 80% residues with mostly side chains. This is not a big structure with no more than 1000 residues in 2 molecules. I wonder why the R values keep so high. Do I need to run anisotropic refinement for such resolutions? Or any other reasons? Thanks!
[ccp4bb] Dashed lines in coot
Hi All, These days I found the model and the density map changed to dashed lines after typed something wrong in the keyboard, I donnot know what have been typed and couldnot change it back to the normal appearance until rerun coot. The version of my coot is 0.3.3 in fedora. Does anybody know about it? Or maybe there is some functions behind those dashed lines? Thanks!
[ccp4bb] phenix.refine and refmac
Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac?
Re: [ccp4bb] phenix.refine and refmac
Yes, I got the mtz file which can be oopened by coot, so can I take the phenix result? I am customed to use refmac before, but now is confused when several choices come out. On 3/4/08, William Scott [EMAIL PROTECTED] wrote: phenix.refine also produces an mtz file by default, and that can be auto-opened with coot, along with the coordinates. On Mar 4, 2008, at 7:27 AM, yang li wrote: Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file.
Re: [ccp4bb] phenix.refine and refmac
Thanks for your replies. I did use default settings in phenix refine, included TLS in it. This is an about 2.3A data, and the number Rfree used to refine is big enough. I also kept the same Rfree in two programs. In refmac I also tried diffenrent weighting sets--from defaut 0.3 to 0.02, TLS included--maybe there are some other ways to define the restrains. The R and Rfree will increase as the weighting is set too low, and the gap didnot improve much. I donnot know in this case if the phenix refine has converged, but the not stable Rfree in refmac made me nervous. Simply, in this case, which one should I choose? Certainly to my private opinion I would prefer to Scott's answer, Rfree is the most obvious parameter than something esle like geometry, eg. Just looks good. :) On 3/5/08, Partha Chakrabarti [EMAIL PROTECTED] wrote: One point which I don't understand is how can someone compare the two different programs when they don't use the same numbers for xray:geometry terms? Taking the default settings for a given resolution might not be enough.. ! On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides [EMAIL PROTECTED] wrote: Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of refinement cycle. Some of the early publications from Axel Brunger on crystallographic cross-validation address the need for enough reflections (500) in the test-set. In addition, the presence of even a handful of strong but inaccurately measured/integrated low-resolution reflections in a limited test-set can aggravate abnormal behavior in R-free. Best wishes Savvas toQuoting yang li [EMAIL PROTECTED]: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
[ccp4bb] Correct the dihedral angles
Dear all, Does anybody have some good experiences or methods to adjust the outlier dihedral angles? I have a model most of which was builded manually, so though the Rfree is acceptable--0.29--manydihedral angles are not right. it is difficult to me to correct them. If there is any software to do it easily, it should be great. Thanks!
[ccp4bb] cns and refmac refinement
Dear All, I have a 3A structure, the quality of the data is not very good. Now I have refined it to Rfree=40.7 in Refmac. But it wonnot go further down. Then I used CNS to do annealing, then use refmac to do rigid body refinement. The Rfree converged to 0.34, but if I use restrain refinement it will go up gradually. Then I use CNS refine script to refine the anneal.pdb, then the rigid body of refmac refinement converged at Rfree=0.33, but the refmac restrain refinement will still increase the Rfree--given weighting=0.03, after 80 cycle Rfree is 0.38 and seems like still increasing. Then I gave weighting=0.02, after 180 cycle, the Rfree is 0.37. I very wonder if I give 1000 cycle to run, Rfree will go back to 0.4. Can anybody give me some suggestions? By the way, it is a dimer and I didnot use NCS restarin during refinement. Below is from refmac log: Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$ $$ 0 0.303 0.3260.738 81869.20.0121.5750.104 1 0.288 0.3370.722 81411.20.0131.3210.080 2 0.284 0.3430.717 81312.90.0111.3030.081 3 0.282 0.3470.713 81308.20.0101.3120.083 4 0.282 0.3490.710 81326.40.0101.3130.083 5 0.281 0.3520.708 81339.90.0101.3210.084 6 0.280 0.3530.707 81356.40.0101.3220.085 7 0.280 0.3550.705 81380.90.0101.3320.086 8 0.280 0.3550.704 81390.50.0101.3300.086 9 0.279 0.3590.702 81400.60.0101.3420.087 10 0.279 0.3570.701 81405.10.0101.3400.086 11 0.279 0.3600.700 81435.30.0101.3490.087 12 0.278 0.3580.700 81425.80.0111.3630.086 13 0.278 0.3620.698 81436.30.0101.3520.087 14 0.278 0.3610.698 81438.10.0101.3470.086 15 0.278 0.3640.696 81456.50.0101.3540.087 16 0.277 0.3630.696 81452.30.0111.3520.087 17 0.278 0.3650.695 81456.70.0101.3560.087 18 0.277 0.3630.695 81450.30.0111.3480.087 19 0.277 0.3660.694 81447.60.0101.3550.087 20 0.276 0.3640.694 81448.20.0111.3500.087 21 0.277 0.3660.693 81451.40.0101.3550.087 22 0.276 0.3640.694 81442.40.0111.3500.087 23 0.277 0.3660.693 81440.80.0101.3540.087 24 0.276 0.3640.693 81434.40.0111.3500.087 25 0.277 0.3650.693 81453.90.0101.3560.087 26 0.276 0.3630.693 81446.50.0111.3520.087 27 0.276 0.3650.693 81448.60.0101.3560.087 28 0.276 0.3630.693 81438.20.0111.3520.087 29 0.276 0.3640.693 81433.70.0101.3560.088 30 0.276 0.3620.693 81430.10.0111.3520.087 31 0.276 0.3640.692 81427.00.0101.3550.087 32 0.275 0.3620.693 81421.20.0111.3540.087 33 0.276 0.3640.692 81428.60.0101.3560.087 34 0.275 0.3620.692 81421.90.0111.3550.087 35 0.275 0.3640.691 81439.00.0101.3580.087 36 0.275 0.3620.691 81435.90.0111.3560.087 37 0.275 0.3640.691 81446.40.0101.3600.088 38 0.275 0.3620.691 81444.60.0101.3580.087 39 0.275 0.3640.690 81453.30.0101.3610.088 40 0.275 0.3620.691 81443.50.0101.3600.087 41 0.275 0.3630.690 81453.20.0101.3620.088 42 0.274 0.3620.691 81443.80.0101.3610.088 43 0.275 0.3640.690 81468.10.0101.3640.088 44 0.274 0.3620.690 81471.50.0101.3630.088 45 0.274 0.3640.689 81509.40.0101.3660.088 46 0.274 0.3630.689 81498.10.0101.3640.088 47 0.274 0.3640.689 81512.90.0101.3680.088 48 0.274 0.3630.689 81499.20.0101.3660.088 49 0.274 0.3650.688 81513.60.0101.3690.088 50 0.274 0.3630.689 81509.30.0101.3680.088 51 0.274 0.3650.688 81505.70.0101.3720.088 52 0.274 0.3630.689
[ccp4bb] Different chains in the dimer
Dear All, I have a protein which has the function unit as a dimer. I got two structures of it. One is the native structure, one is the mutant structure. Both structures are dimer in ASU. In the native structure the two chain look the same, but in mutant structure one chain still keep the same structure as the native one, and another chain is different. We expect to see the difference, but we wonder why one chain is different and another one is the same? Is this because of crystallographic packing? Thanks!
[ccp4bb] ideal bond length and bong angel
Dear All, I've wonder for a simple problem for a long time, that is: What is the ideal bond length and angel? Every lecture or book says this is a criteria from small organic molecules, but I still donnot know exactly. Like is bond length point to the peptide bond length? Or many other bonds? Does anyone has a simple and graphic explanation for them? Thanks in advance!
Re: [ccp4bb] ideal bond length and bong angel
By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calculate the C=N bond, and donnot know which one is used as the aggel. It should be a quite stupid question for whom knows it. Just forget it.
Re: [ccp4bb] ideal bond length and bong angel
Dear Prof Gerard: In fact I have read your Model Validation on-line, and I have to say it is youe lecture that made me to think about this problem, though I have used it as a common stand for the quality of the model without understand it for a long time. And the http://en.wikipedia.org/wiki/Molecular_geometry and http://en.wikipedia.org/wiki/Dihedral_angle, I think both from your lecture, I have checked them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed with others before, so I just want to make it clear, though maybe nothing to do with practicals. Thanks for your reply again. Best Regards!
[ccp4bb] apologize
Dear All, I am very sorry to involve you into such insignificance discussion, I have reached agreement with Prof Gerard, please stop talking about things beyond science, thanks! I read a book today, which said A refined model should exhibit rms deviations of no more than 0.02A for bond length and 4 for bond angels, I just wonder about the standard of the bond length and the bond angel. I think most of you have read similar words! But maybe I didnot express clearly and made some phrasal mistakes. At last, happy new year to you all--though very late! Sincerely! Yang Li
Re: [ccp4bb] scalepack problem
Hi,All, I have figured out the mistake, for some reason some -h,-k,-l reflections were missed for the spacegroup given, so the program was not happy with the format. I donnot know how it happened since not me processed the data. Then another question is how the scale porgrams do with the situation that one of the friedel pair is missed? Does it discard these reflecions for the anomalous file and retain them for the isomophous file? Thanks!
Re: [ccp4bb] scalepack problem
On Dec 31, 2007 4:06 PM, Noinaj, Nicholas [EMAIL PROTECTED] wrote: Hi, would it be possible for you to send me either your *.sca file or at least just the first 50 lines or so? i have experienced this problem before also, but all i had to do was removed an alpha numerical sequence in the header, which scalepack put there for some reason. only happened a time or two though. which program do you use to process your data? just wonderingbest of luck! cheers, nick From: CCP4 bulletin board [EMAIL PROTECTED] On Behalf Of yang li [ [EMAIL PROTECTED] Sent: Monday, December 31, 2007 12:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] scalepack problem Hi All, Thanks for your replies. I think the problem shouldnot be spacegroup because I tried several other spacegroups(just modify the sca file or specify in the script), the resluts are the same. the error is: Sort Order : 0 0 0 Spacegroup = 'p1' (number=1) Scalepack2mtz: check you data # I deleted some lines because I tried to find where are the problems. The format looks has no problem. Only if I retain very few reflctions it worked, when I added some others lines(different lines) , it would go wrong. And this file can be used in phenix without problem.I would like to try Abendroth's suggestion after I install CNS. Thanks again!
[ccp4bb] problem while installing CNS1.2
Dear All, When I tried to install cns, I met such error, I asked other people, no one has seen this before, so maybe someone here had similiar problem or method to solve it: compiling: initia.f compiling: lbfgs.f compiling: lidens.f compiling: machine_f.f In file machine_f.f:393 ERR=.TRUE. 1 In file machine_f.f:297 2 Error: Label at (1) is not in the same block as the GOTO statement at (2) make[3]: *** [machine_f.o] 错误 1 compiling: machvar.f compiling: mapyard.f compiling: matrix.f .. compiling: dmemory.c compiling: machine_c.c make[3]: 由于错误目标../bin/cns_solve并未重新创建。 make[2]: *** [cns_solve] 错误 2 make[1]: *** [cns_solve] 错误 2 ##3 Thanks in advance!
Re: [ccp4bb] scalepack problem
Hi All, Thanks for your replies. I think the problem shouldnot be spacegroup because I tried several other spacegroups(just modify the sca file or specify in the script), the resluts are the same. the error is: Sort Order : 0 0 0 Spacegroup = 'p1' (number=1) Scalepack2mtz: check you data # I deleted some lines because I tried to find where are the problems. The format looks has no problem. Only if I retain very few reflctions it worked, when I added some others lines(different lines) , it would go wrong. And this file can be used in phenix without problem.I would like to try Abendroth's suggestion after I install CNS. Thanks again!
[ccp4bb] scalepack problem
Hi All, I met a problem while running scalepack2mtz in ccp4 interface. The program will stop with a tip said check your data, but no error warning. This SCA file is a H3 spacegroup but maybe it is not because the spacegroup since if I use p1 had the same problem. I tried to delete some lines from the file then it worked. I really cannot find how those lines made the file bad, they had nothing abnormal to me. Thanks for your help!
[ccp4bb] Cif file in coot
Hi All, If I have a pdb with some residues named abc in it, coot can read it and display it well, but I cannot do real space refine to such residues. The tips asks me to import a CIF file, I wonder what is the format of this CIF file? How can I create it and let coot recognise these residues? Or there are some other ways to solve it? Thanks!
[ccp4bb] How to show density map in pymol?
Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!
[ccp4bb] How to run ccp4 in php script?
Hi All, I have some scripts which need to use some programs--like cad, refmac--in ccp4, and I want to use a php script to run these scripts, with command as : $cmd = sh aa.inp; system($cmd); As I know, when I use php script, the account is Apache, which is a nologin account, all the files I used are put in the directory which belong to Apache.I donnot know what shell it uses, assume it uses bash, since Apache has no permission to /ccp4/include/ccp4.setup, I copied ccp4.setup to the directory I used. And add a line in the script to source this ccp4.setup, file, but it gives such error information: * WARNING ** The directory /home/prog/ccp4 (assigned to CCP4_MASTER) does not exist. The CCP4 programs will not run correctly, and any installation attempt will have errors or will fail. * WARNING ** I donnot know how to solve this problem. Anyone knows how to run the ccp4 programs with the php script? Thanks!
[ccp4bb] problem with HKL2000 license
Hi,All, Now I am installing HKL2000 and met a curious problem: The license cr_info was apllied before, the system is fc6 at that time. Before received the license, I reinstalled the system for some reason, now the system is fc4. the install files and anom.dat file was copied from other people. I changed all the configs,now if I run access_prod file the values of HOST-NAME, HOST-ID,HOSTNAME,HW-PROV,CPU-SERIAL are all same with the values when apllied the license. But now if I type HKL2000, comes the error information: ERROR: Not a valid HKL-2000 license: Problem with hardware recognition *Field HOST-NAME * *Error code: 6* ** *I googled for this error, the answer is: HOST-NAME line in the info file must have changed. Please re-run the access_prod program on that computer and send to [EMAIL PROTECTED] Your access file, cr_info, needs to be updated.* ** * I wonder if I rerun the access_prod programm, the hostname is the same, how could it give this error?* It is a little troublesome if have to update the license, so I think if anyone can tell the reason, it will save much work. Best Regards
[ccp4bb] How to run Java program?
Hi,
I have a java program named Switch.java, I want to run it under fedora5
core, I donnot know any compiler
I need to install? I installed a package named jre-1_5_0_11-
linux-i586-rpm.bin, when I use command
java Switch.java
wrong information came out:
Exception in thread main java.lang.NoClassDefFoundError: SwitchI
at gnu.java.lang.MainThread.run(libgcj.so.7)
Caused by: java.lang.ClassNotFoundException: SwitchI not found in
gnu.gcj.runtime.SystemClassLoader{urls=[file:./], parent=
gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}
at java.net.URLClassLoader.findClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.Class.forName(libgcj.so.7)
at gnu.java.lang.MainThread.run(libgcj.so.7)
Then I used command yum install libgcj.so.7 , but it was not helpful.
I am a java newhand, any help will be appreciated, thanks!
[ccp4bb] Question about cryoprotectant
Hi, l have a crystal grow at condition screen l 40: 0.1M tri-sodium citrate dihydrate pH5.6 isoproponal 20%PEG4k 20% and the crystal need a cryoprotectant, we have used the 30% glycerol but it is not good, the mosaicity of the diffraction pattern is a little high, so anyone knows which is the best cryoprotectant for this crystal? Thanks!
[ccp4bb] phaser in ccp46.0.2
Hi, Anyone has used phser in ccp46.0.2 which is automatically installed with ccp4? In previous ccp4 edition I installed phaser seperately and it worked well, but now it seems has some problems, it cannot read the input mtz file, I tried several data, all gave the same error information like below: * *** Phaser Module: READ DATA FROM MTZ FILE2.0 *** * BFONT COLOR=#FF8800 --- FILE OPENING ERROR: /root/work/1she/1she.mtz --- /FONT/B EXIT STATUS: FAILURE I donnot think all these data are bad, and these data can be read in other mr programs. I wonder if I should install phaser again? The phaser install package for CCP4-5.0 still can be used in this edition? Thanks!
[ccp4bb] Scale factor in ccp4
Hi: I have two set of data from the same crystal with the names 1.sca and 2.sca, they have different Intensity values due to different scale factors. Now I use Scalepack2mtz convert them to 1.mtz and 2.mtz, then use cad to merge to a cad.mtz, then convert it to cad.sca file, I find that the Intensity values in this cad.sca arediffrent from 1.sca and 2.sca, I wonder if the program has scaled the values itself? If that is true, which program did this, Scalepack2mtz or cad? Thanks! Li Yang
[ccp4bb] question about redundancy
Hi: I am confused by a idea for a long time, and it maybe an easy question. That is, if a cryst with p1 spacegroup, after 360 degree data collection, what the redundancy should be? I was told that it is 2, and the 2 are F(h,k,l) and F(-h,-k,-l), but I think if the reciprocal lattice rotated 360 degree, it must intersect with the ewald sphere 2 times--for example, go into the sphere and go out--then F(h,k,l) should be collected twice. I donnot know what is wrong with my option. Anyone can tell me the reason? Thanks! Li Yang
[ccp4bb] refmac refinement and multiple conformations
If a pdb file contains some residues that have multiple conformations, when using refmac to refine it, will the programm take consider of these conformations? It seems that refmac would do this but I am not very sure. I downloaded a structure with some conformations from the pdb, but after refmac the R free is not as low as on the website. What is the problem? Thanks! Li Yang
[ccp4bb] compiler question
When I installed a programm, it gave such information: ./install.sh /usr/bin/ld: cannot find -lstdc++ collect2: ld returned 1 exit status make: *** [Linux] Error 1 Is it because of absence of some compilers? How can I install it? I am using the Fedora5 system. Thanks! Li Yang
[ccp4bb] weighting term in refmac
Hi, There is a value of weighting term with default 0.3 in refmac5, what is the exact meaning of it? What is the best value of it for different resolution data? Does it affect the result R value much? Li Yang
[ccp4bb] Mtz2various
Hi: I'd use Mtz2various to convert .mtz file to .phs format. The format of .phs file is like below: 0 0 9 29.5 0.14 220.00.00.00.00.0 0 0 12 160.5 0.97 109.0 -4.52.4 -0.91.2 0 0 15 72.6 0.87 56.0 36.5 10.5 -12.6 -7.9 0 0 18 195.6 0.98 133.0 -0.84.40.70.3 0 0 21 149.7 0.98 143.0 -9.44.6 -0.50.6 0 0 24 245.6 0.98 89.01.92.30.2 -1.3 proces How should I define the Ouput Fortran format? I used '(3i4,7f7.1)' and made the first three columns processed as generic int, others generic real, but the result was not right like the model,. Thanks Li yang
