Re: [ccp4bb] Error message while refining protein-DNA complex structure in Refmac5
Hi Rajkumar, Few days back similar problem was happening to me also. I just changed the version of Coot and it worked. In my case only Coot (ver. 4.1) was doing the job correct. Please try Coot (version 4.1) in case you are using any of other versions. HTH, Y On Mon, Mar 16, 2009 at 11:43 PM, E rajakumar wrote: > Dear All > I am refining proitein-DNA complex structure in > Refamac5. When I used coordinate file containing 2 > bases less, then the refinement is running smoth and > perfect. But when I built 2 exta bases to the existing > DNA in the coot then refinement is failed with the > following error message. > > /usr/local/ccp4-6.1.0/bin/refmac5 > XYZIN"/usr6/rajkumar/APS/hem/mar9/H2/molrep/BCDNA-built2-NCS-refm2.pdb" > XYZOUT "/tmp/rajkumar/hemCG_19_2_pdb_1.tmp" HKLIN > "/usr6/rajkumar/APS/hem/mar9/H2/molrep/P6122.mtz" > HKLOUT "/tmp/rajkumar/hemCG_19_3_mtz_1.tmp" LIBOUT > "/usr6/rajkumar/APS/hem/mar9/H2/molrep/hemCG_19_lib.cif" > > has failed with error message > At line 2486 of file > /usr/local/xtal/ccp4-6.1.0/src/refmac5_/make_PDB.f > Fortran runtime error: Bad value during floating point > read > > It seems there is error in LIB file generation. > Coordinate format and atom labelling is accoring to > refmac convention. > > Please can anybody suggest me how do I trooubleshoot. > > Thanking you > Rajakumara > > > > > E. Rajakumara > Postdoctoral Fellow > Strcutural Biology Program > Memorial Sloan-Kettering Cancer Center > New York-10021 > NY > 001 212 639 7986 (Lab) > 001 917 674 6266 (Mobile) > > > > Get your preferred Email name! > Now you can @ymail.com and @rocketmail.com. > http://mail.promotions.yahoo.com/newdomains/aa/ > -- * Present Address: Yusuf Akhter, DAAD Fellow EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Mobile: +49-17676339706
Re: [ccp4bb] Coot Problem! adding r-nucleotide in DNA
Thanks to Paul and Christian..for responding very quickly to my query. I tried all versions of coot and it worked in only ver 0.4. Now everything is fine. Cheers! Yusuf On Thu, Feb 26, 2009 at 7:04 PM, Yusuf Akhter wrote: > Hi everybody! > I am using coot version 0.5. > I am trying to build a DNA sequence in my model. > > At certain positions when i add residues and then used "simple mutate" to > make it according to real sequence, it always add ribonucleotide (guanine > ribonucleotide, Gr) in place of deoxyribonucleotide (guanine deoxynucleotide > Gd). When i say "add residue" it adds adenine deoxynucleotide but on using > "simple mutate" function this problem occurs. > > In rest of the positions in sequence everything works fine except at this > particular position. > > have anybody faced similar problem?? > > Any suggestion will be appreciated. > > > Thanks in advance. > > > Yusuf > > > > > > > > > >
[ccp4bb] Coot Problem! adding r-nucleotide in DNA
Hi everybody! I am using coot version 0.5. I am trying to build a DNA sequence in my model. At certain positions when i add residues and then used "simple mutate" to make it according to real sequence, it always add ribonucleotide (guanine ribonucleotide, Gr) in place of deoxyribonucleotide (guanine deoxynucleotide Gd). When i say "add residue" it adds adenine deoxynucleotide but on using "simple mutate" function this problem occurs. In rest of the positions in sequence everything works fine except at this particular position. have anybody faced similar problem?? Any suggestion will be appreciated. Thanks in advance. Yusuf
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] 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/
[ccp4bb] Refmac out-put file header information
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 > > -- > Yusuf Akhter > EMBL Hamburg c/o DESY, Notkestraße 85, > 22603 Hamburg, Germany > - This mail sent through IMP: http://horde.org/imp/
[ccp4bb] D-Amino acids to L-Amino acids
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 -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/
[ccp4bb] D-Amino acids to L-Amino acids
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 -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/
