[ccp4bb] pseudo-translation vector in molrep
Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html
Re: [ccp4bb] pseudo-translation vector in molrep
I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01 but it must be too close to the origin to be a translation vector from one molecule to another. There are reasons for such peaks - sometimes spurious large terms in the data.. but they dont usually represent true molecular translations. Trust MOLREP! Eleanor Savvas Savvides wrote: Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] _http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html_
[ccp4bb] problem in running DM (NCS averaging)
Dear all, I tried to run DM for NCS averaging (DM module in CCP4i 6.0.2 installed under Windows XP), but the running failed at different stages with various error message as listed below. I was told it could be an installation problem, but I don't know how to fix it. I am wondering if you have encountered such problems before. I am very thankful for any help and comments. Thanks in advance. Error Message 1: * #CCP4I JOB_ID 69 #CCP4I SCRATCH C:/Ccp4Temp/ #CCP4I PID 772 /pre BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B a name=dmdmh1dm 2.1/h1/a BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.0: dm version 6.0 : ## ### User: Chen Run date: 30/ 7/2007 Run time: 10:27:58 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B /pre a href=http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html;dm reference:/a blockquote K. Cowtan (1994), dm: An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38. /blockquotep a name=tocdmh2Contents/h2/a ul lia href=#commanddmCommand input/a lia href=#commentsdmComments/a lia href=#mtzindmMTZ input/a lia href=#datachkdmData Checking/a lia href=#datascldmData Scaling/a lia href=#solmskdmSolvent Mask/a lia href=#cyc0001dmFirst Cycle/a lia href=#dataoutdmOutput/a /ul a name=commanddmh2Command Input/h2/a pre Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#modeMODE /a SOLV AVER Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#combineCOMBINE /a PERT Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#ncsmaskNCSMASK /a SIZE 10 Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#schemeSCHEME /a ALL Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#ncycleNCYCLE /a AUTO Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#solcSOLCONT /a 0.5 Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#averageAVERAGE /a REFI *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid keyword *** Warning Invalid sub-keyword in position 2 *** Warning Invalid sub-keyword in position 3 *** Warning Invalid sub-keyword in position 4 *** Warning Invalid sub-keyword in position 5 *** Warning Invalid sub-keyword in position 6 *** Warning Invalid sub-keyword in position 7 *** Warning Invalid sub-keyword in position 8 *** Warning Invalid sub-keyword in position 9 Data line--- a href=C:\CCP4-Packages\ccp4-6.0.2\html/dm.html#laboutLABOUT /a FDM=FDM PHIDM=PHIDM FOMDM=FOMDM BFONT COLOR=#FF!--SUMMARY_BEGIN-- dm: Input error (see above) Times: User: 0.0s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B *** * Information from CCP4Interface script *** The program run with command: dm HKLIN D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_refmac7.mtz HKLOUT D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm4.mtz SOLOUT D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm2.msk NCSIN1 D:/xtalwork/DM21/delM_arpwarp/work1/A.msk VUOUT D:/xtalwork/DM21/delM_arpwarp/work1/delM_69_ncs.odat has failed with error message dm: Input error (see above) *** #CCP4I TERMINATION STATUS 0 dm: Input error (see above) #CCP4I TERMINATION TIME 30 Jul 2007 10:27:58 #CCP4I MESSAGE Task failed Error Message 2: +++ a name=ncsmskdmh3Initial Averaging Mask/h3/a BFONT COLOR=#FF!--SUMMARY_BEGIN-- *** * Information from CCP4Interface script *** The program run with command: dm HKLIN D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_refmac7.mtz
Re: [ccp4bb] pseudo-translation vector in molrep
Hi, I suggest you check which version of MOLREP you used. Currently, BALBES now actually use MOLREP in 'auto' mode for PST. The two should be the same. The difference may be because BALBES uses the latest version of MOLREP. Fei On 7/30/07, Eleanor Dodson [EMAIL PROTECTED] wrote: I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01 but it must be too close to the origin to be a translation vector from one molecule to another. There are reasons for such peaks - sometimes spurious large terms in the data.. but they dont usually represent true molecular translations. Trust MOLREP! Eleanor Savvas Savvides wrote: Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] _http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html_
[ccp4bb] DNase inhibitors
Hi all, I have small crystals of protein DNA complex. I am worried about the possibility of presence of some DNases in the drop (I use DNase in the lysis buffer). I have Tris and MgCl2 in the crystallization condition, which makes me hesitant to use DEPC or EDTA/EGTA respectively. Are there any other DNase inhibitors that I can use to protect the DNA? Any other precautions one should take while handling DNA Thank you Kumar Dept. of Biochemistry, Cellular and Molecular Biology, Walters Life Science, # 406, University of Tennessee, TN, Knoxville, USA
Re: [ccp4bb] DNase inhibitors
I have small crystals of protein DNA complex. I am worried about the possibility of presence of some DNases in the drop (I use DNase in the lysis buffer). I have Tris and MgCl2 in the crystallization condition, which makes me hesitant to use DEPC or EDTA/EGTA respectively. Are there any other DNase inhibitors that I can use to protect the DNA? Any other precautions one should take while handling DNA There is something called aurintricarboxylic acid that I've seen mentioned several times. it is supposed to be a general inhibitor of nucleases. I have no experience with it. Also, this may sound crazy but if you are worried about DNAse I that you used in previous steps, one option is to add a little bit of actin. Actin binds to DNAse I very specifically and with very high affinity, inhibiting its activity. At the concentrations that you are likely to use it at, it should be below critical concentration that makes it polymerize. Dima
