Re: [ccp4bb] Problem converting CNS cv file to mtz using f2mtz
CNS format changes with the time of day and unfortunately f2mtz requires
that you give a correct fortran format stt.
This command script works from the GUI:
Note that
1) you must the "skip lines"
2) you need X entries to skip unwanted characters . These include INDE
(7x) FOBS= (6x) and also
the second entry after FOBS which is in this case always 0.000 so the
17X skips that pluse SIGMA=
3) and since TEST= is on a second line you need the / to indicate this.
Kevin Cowtan has a clipper utility which is clever and does not require
the format stt - it reads the header and works out what will follow from
that. IT is available from here:
He writes:
This is a replacement for cns2mtz, which fixes all the reported bugs in
that program, is rather more convenient, and handles other ascii file
types as well, including at least SHELX hkl files and XtalView PHS files.
Changes include:
- Spacegroup headers are now generated correctly. (I hope).
- Column names may be speicified for non-CNS files or CNS files with
missing headers.
- If a file contains F+/- or I+/- without sigmas (e.g. CNS density
modified data), then dummy columns of sigmas are added automatically.
Any further problems, please let me know!
http://www.ysbl.york.ac.uk/~cowtan/convert2mtz/convert2mtz.html
***
/tmp/ccp4/acornmr2_412_2_com.tmp
***
title TRIAL 3
symmetry P1
cell 26.65 30.8 33.63 89.3 107.4 112.2
format '(7X,3F5.0,6X,F10.3,18X,F10.3,/,5X,F10.0)'
skipline 5
labout H K L FP SIGFP FreeRflag
ctypout H H H F Q X
PNAME acornmr2
DNAME trial3
XNAME trial3
end
## This script run with the command ##
# f2mtz HKLIN "/y/people/ccp4/x.cv" HKLOUT
"/tmp/ccp4/acornmr2_412_1_mtz.tmp"
Ryan Watkins wrote:
Hello Colleagues,
I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
Fobs and SigFs. Unfortunately, I cannot get f2mtz to work and am
looking for some help. The program dies either with a "cannot read
first reflection" or with a "child killed: bus error" error. Here are
the 1st few lines of my file:
NREFlection=140763
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
INDE -4601 FOBS=63.800 0.000 SIGMA=33.060
TEST= 0
INDE -4602 FOBS= 168.800 0.000 SIGMA=19.440
TEST= 0
INDE -4603 FOBS= 331.700 0.000 SIGMA=13.850
TEST= 0
INDE -4611 FOBS= 210.000 0.000 SIGMA=13.400
TEST= 0
INDE -4612 FOBS= 297.800 0.000 SIGMA=11.830
TEST= 0
INDE -4501 FOBS= 559.100 0.000 SIGMA=18.030
TEST= 1
INDE -4502 FOBS= 500.400 0.000 SIGMA=16.800
TEST= 0
Thank you,
Ryan
Ryan Watkins
Postdoctoral Fellow
Brennan Lab
MD Anderson Cancer Center
[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 dm 2.1 ### ### ### ### 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. http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html";>dm reference: 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. Contents Command input Comments MTZ input Data Checking Data Scaling Solvent Mask First Cycle Output Command Input Data line--- MODE SOLV AVER Data line--- COMBINE PERT Data line--- NCSMASK SIZE 10 Data line--- SCHEME ALL Data line--- NCYCLE AUTO Data line--- SOLCONT 0.5 Data line--- AVERAGE 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--- LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM dm: Input error (see above) Times: User: 0.0s System:0.0s Elapsed: 0:00 *** * 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: +++ Initial Averaging Mask *** * 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_dm3.mtz" SOLOUT "D:/xtalwork/DM21/delM_arpwarp/work1/7_solvent_dm2.msk" NCSOUT "D:/xtalwork/tmp/delM_63_ncs.msk" has failed with error message forrtl: severe (157): Program Exception - access violation Image PCRoutineLine Source ntdll.dll 7C911E58 Unknown Unknown Unknown ntdll.dll 7C910D5C Unknown Unknown Unknown dm.exe 004A8FFF Unknown Unknown Unknown *** #CCP4I TERMINATION STATUS 0 "forrtl: severe (157): Program Exception - access violation Image PCRoutine LineSource ntdll.dll 7C911E58 Unknown Unknown Unknown ntdll.dll 7C910D5C Unknown Unknown Unknown dm.exe 004A8FFF Unknown Unknown Unknown" #CCP4I TERMINATION TIME 29
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
