Re: [ccp4bb] Refmac out-put file header information
Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 12072 Have anybody some suggestions?? Thanks, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Thank you very much to Artem, Lijun, Dale and Paul for giving me great suggestions regarding my earlier query on D to L amino acid residues. Now one more problem is in same 3 A structure refinement. For those who not remembered my case. I have processed a diffraction data-set at 3 A using XDS. I am using Refmac for refinement. My data is 95.4% of completeness at Signal/noise =-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Is it a bug?? May somebody tell me where the problem is? Thanks in advance. yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Quoting Yusuf Akhter [EMAIL PROTECTED]: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf - This mail sent through IMP: http://horde.org/imp/
Re: [ccp4bb] Refmac out-put file header information
Hi Yusuf, You need to run the uniqueify script to expand the input file to include all possible reflections (observed and missing from your data set). I have not run xdsconv with the GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 However, generally after running xdsconv without that command, it is necessary to run f2mtz, cad and uniqueify to prepare the input file for refmac. You can do a quick test like mtzdump test.mtz if it reports that your Fobs are 100% complete, then you need to run uniqueify to expand the file to contain all possible reflections up to the highest resolution in your input file. Without this, then the statistics will not be reported correctly in refmac and many other programs. see http://www.ccp4.ac.uk/dist/html/refmac5/files/log.html#pobs Percentage observed Fraction of the observed reflections in %. If uniqueify has been run before using REFMAC, this value will be calculated correctly. Otherwise it will be 100.0%. If your free flag column label is FreeRflag, then you can run the uniqueify script from the command line like: uniqueify -p 0.05 -f FreeRflag test.mtz if your input file is test.mtz the output from the script will be test-unique.mtz. or you can use the ccp4i task merge mtz files (CAD) by inputting your existing .mtz file and checking the box to complete the reflection list and extend your input freeR set. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf Akhter Sent: Friday, August 08, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac out-put file header information Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 12072 Have anybody some suggestions?? Thanks, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Thank you very much to Artem, Lijun, Dale and Paul for giving me great suggestions regarding my earlier query on D to L amino acid residues. Now one more problem is in same 3 A structure refinement. For those who not remembered my case. I have processed a diffraction data-set at 3 A using XDS. I am using Refmac for refinement. My data is 95.4% of completeness at Signal/noise =-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Is it a bug?? May somebody tell me where the problem is? Thanks in advance. yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Quoting Yusuf Akhter [EMAIL PROTECTED]: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf - This mail sent through IMP: http://horde.org/imp/
Re: [ccp4bb] Refmac out-put file header information
Hi Mitch, When i checked carefully again log files. I came to know that, when i used xdsconv then only the total completeness have been changed from 95% to 100%. Before xdsconv all log-files have original 95%. Now what should i do?? thanks, yusuf Quoting Miller, Mitchell D. [EMAIL PROTECTED]: Hi Yusuf, You need to run the uniqueify script to expand the input file to include all possible reflections (observed and missing from your data set). I have not run xdsconv with the GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 However, generally after running xdsconv without that command, it is necessary to run f2mtz, cad and uniqueify to prepare the input file for refmac. You can do a quick test like mtzdump test.mtz if it reports that your Fobs are 100% complete, then you need to run uniqueify to expand the file to contain all possible reflections up to the highest resolution in your input file. Without this, then the statistics will not be reported correctly in refmac and many other programs. see http://www.ccp4.ac.uk/dist/html/refmac5/files/log.html#pobs Percentage observed Fraction of the observed reflections in %. If uniqueify has been run before using REFMAC, this value will be calculated correctly. Otherwise it will be 100.0%. If your free flag column label is FreeRflag, then you can run the uniqueify script from the command line like: uniqueify -p 0.05 -f FreeRflag test.mtz if your input file is test.mtz the output from the script will be test-unique.mtz. or you can use the ccp4i task merge mtz files (CAD) by inputting your existing .mtz file and checking the box to complete the reflection list and extend your input freeR set. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf Akhter Sent: Friday, August 08, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac out-put file header information Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 12072 Have anybody some suggestions?? Thanks, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Thank you very much to Artem, Lijun, Dale and Paul for giving me great suggestions regarding my earlier query on D to L amino acid residues. Now one more problem is in same 3 A structure refinement. For those who not remembered my case. I have processed a diffraction data-set at 3 A using XDS. I am using Refmac for refinement. My data is 95.4% of completeness at Signal/noise =-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Is it a bug?? May somebody tell me where the problem is? Thanks in advance. yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Quoting Yusuf Akhter [EMAIL PROTECTED]: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf - This mail sent through IMP: http://horde.org/imp/ - This mail sent through IMP: http://horde.org/imp/
Re: [ccp4bb] interface
Which brings up something about PISA. If I run PISA on pdb entry 2IE3, which I'm familiar with, I get the following numbers from PISA and CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface. PISA for 2IE3 Automatic A:C interface selection 907.9 (a crystal packing interface is larger than this, but this surface is the A:C interface) AreaIMol with some editing of 2IE3 to separate the chains Chain A25,604.4 Chain C11,847.4 Total 37,451.8 Chain AC 35,576.6 Difference 1,875.2 Difference/2 937.6 For buried S.A. I agree with Steve Darnell's definition. However PISA appears to be reporting half that value, or what it calls interface area. Potentially confusing. Phil Jeffrey Princeton Steven Darnell wrote: Sorry, that equation should read: Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound ASA = Accessible Surface Area The way I wrote it before would give you a negative value. Regards, Steve Darnell
Re: [ccp4bb] interface
Phil, I had a follow up conversation regarding this very topic. Here is an excerpt: The following is from Chothia and Janin (1975) Nature, 256:705-708, one of the early articles regarding buried surface area and protein interfaces: The surface area buried in the complex is then defined as the accessible surface area of one subunit plus that of the other subunit minus that of the complex. I believe that definition has not changed in 30 years. While I will agree that dividing by 2 approximates the physical area of the interface, this does not represent the total amount of surface area that is no longer accessible to solvent. In terms of desolvating the interface for binding, the latter is more appropriate. As you point out, PISA appears to be reporting the area of the interface, not the total surface area occluded from solvent. Confusing indeed. Regards, Steve Darnell Phil Jeffrey said the following on 8/8/08 10:03 AM: Which brings up something about PISA. If I run PISA on pdb entry 2IE3, which I'm familiar with, I get the following numbers from PISA and CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface. PISA for 2IE3 Automatic A:C interface selection 907.9 (a crystal packing interface is larger than this, but this surface is the A:C interface) AreaIMol with some editing of 2IE3 to separate the chains Chain A25,604.4 Chain C11,847.4 Total 37,451.8 Chain AC 35,576.6 Difference 1,875.2 Difference/2 937.6 For buried S.A. I agree with Steve Darnell's definition. However PISA appears to be reporting half that value, or what it calls interface area. Potentially confusing. Phil Jeffrey Princeton -- Steven Darnell Department of Biochemistry University of Wisconsin-Madison Madison, WI USA
[ccp4bb] April fools hand issue solved
Dear crystallographers, although many laughed off one CCP4BB poster's comments several months ago as an April fools' trick (he had proposed that Bijvoet had actually botched the job, as I remember), there is now apparently experimental evidence against that trick: Was Bijvoet right? Sodium rubidium (+)-tartrate tetrahydrate revisited.Lutz M, Schreurs AM. Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. The first determination of the absolute configuration of an organic compound was published in 1951 on sodium rubidium (+)-tartrate tetrahydrate, Na(+).Rb(+).C(4)H(4)O(6)(2-).4H(2)O, but the atomic coordinates are not available in the public literature. This structure has therefore been redetermined using current equipment. The most up-to-date techniques for the determination of the absolute configuration have been applied and the question posed in the title can be answered with an unequivocal ;yes'. JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
Re: [ccp4bb] interface
The way I look at it; BSA the the total surface area defined within two bisecting 3D curves, interface area is the minimum surface area that can be that can be produced by interpolation between regions at bisect each other. Probably not the best definition. On a side note: can one really use this approach to calculate BSA between domains? I could see a situation where splitting domains into two separate entities would calculate excess surface area for regions that connect these domains. I recall using Insight2 ages ago to create subsets, and then calculating Connolly surfaces within a given context. From what I remember, it was real pain. Any better software out there for this? Cheers, AGS Date: Fri, 8 Aug 2008 11:03:59 -0400 From: [EMAIL PROTECTED] Subject: Re: [ccp4bb] interface To: CCP4BB@JISCMAIL.AC.UK Which brings up something about PISA. If I run PISA on pdb entry 2IE3, which I'm familiar with, I get the following numbers from PISA and CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface. PISA for 2IE3 Automatic A:C interface selection 907.9 (a crystal packing interface is larger than this, but this surface is the A:C interface) AreaIMol with some editing of 2IE3 to separate the chains Chain A25,604.4 Chain C11,847.4 Total 37,451.8 Chain AC 35,576.6 Difference 1,875.2 Difference/2 937.6 For buried S.A. I agree with Steve Darnell's definition. However PISA appears to be reporting half that value, or what it calls interface area. Potentially confusing. Phil Jeffrey Princeton Steven Darnell wrote: Sorry, that equation should read: Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound ASA = Accessible Surface Area The way I wrote it before would give you a negative value. Regards, Steve Darnell _ Reveal your inner athlete and share it with friends on Windows Live. http://revealyourinnerathlete.windowslive.com?locale=en-usocid=TXT_TAGLM_WLYIA_whichathlete_us
[ccp4bb] merohedral twinning problem
Dear, Sorry for the off-topic question. I'm facing a (probably) merohedral twinning problem, regarding a small molecule. Using Xprep, I get a Hexagonal P-lattice with cell: 18.014 18.014 22.048 90.00 90.00 120.00 Mean |E*E-1| = 0.902 [expected .968 centrosym and .736 non-centrosym] However, based on the systematic absence exceptions, the probable (apparent) SG's are: P6(3)/m (Laue '6/m') P6(3) (Laue '6') P6(3)22 (Laue '622') 61/65 62=31 63-c- --c N60 50 36 2471 1420 N I3s 19 19 0 420 161 I186.6 223.1 4.6 30.015.5 I/s 2.3 2.6 0.3 1.6 1.2 I know there is a twin law to transform the (apparent) Laue group '6/ m' to the (true) Laue group '-3' (TWIN law -1 0 0 0 -1 0 0 0 1) and merging the data in a trigonal SG, but this is not solving the structure at all... Has anyone noticed a similar case that could be of any help please..? Many thanks Kristof Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] stereo in coot with RHEL 5
Hi- There seems to be a problem enabling stereo with coot on RHEL 5, which results in the error: CATASTROPHIC ERROR:: in gl_extras no GtkGL widget! WARNING:: switch to hardware_stereo_mode failed I've found mention of this through a google search, but no solution. Has anyone encountered this and found a way to fix it? I'm using an NVIDIA Quadro FX 3500 with an xorg.conf identical to an RHEL 4 system on which stereo works. I assume it has to do with this system being 64-bit rather than 32-bit. Thanks in advance for any help! --James
Re: [ccp4bb] April fools hand issue solved
Could be a case of modeler bias. Just look at the name of the institute. This is like having a Jessie Helms endowed chair in the therapeutic benefits of tobacco. On Aug 8, 2008, at 8:31 AM, Jacob Keller wrote: Dear crystallographers, although many laughed off one CCP4BB poster's comments several months ago as an April fools' trick (he had proposed that Bijvoet had actually botched the job, as I remember), there is now apparently experimental evidence against that trick: Was Bijvoet right? Sodium rubidium (+)-tartrate tetrahydrate revisited.Lutz M, Schreurs AM. Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. The first determination of the absolute configuration of an organic compound was published in 1951 on sodium rubidium (+)-tartrate tetrahydrate, Na(+).Rb(+).C(4)H(4)O(6)(2-).4H(2)O, but the atomic coordinates are not available in the public literature. This structure has therefore been redetermined using current equipment. The most up-to-date techniques for the determination of the absolute configuration have been applied and the question posed in the title can be answered with an unequivocal ;yes'. JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
[ccp4bb] map coefficients - origin shift
Dear all, Is there a program, which will shift the origin of a set of mtz map-coefficients by means of a fractional coordinate vector R? Thanks, -Martin -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA
