[ccp4bb] Error message while refining protein-DNA complex structure in Refmac5
Dear Garib Thank you. After removing SCALE card in the pdb file, refinement is completed somthly. Rajakumara --- Garib Murshudov ga...@ysbl.york.ac.uk wrote: It seems that something may be wrong with your input file. Specifically with the SCALE card in the pdb file. Could you please remove SCALE lines from the pdb and try again. If it does not help then could you please send me your pdb file and I will try to sort out. Garib On 16 Mar 2009, at 22:43, 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/ 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/
Re: [ccp4bb] Error message while refining protein-DNA complex structure in Refmac5
Dear Garib Thank you very much as you suggested, I removed SCALE card in the pdb file, then it is running smothly. Rajakumara --- Garib Murshudov ga...@ysbl.york.ac.uk wrote: It seems that something may be wrong with your input file. Specifically with the SCALE card in the pdb file. Could you please remove SCALE lines from the pdb and try again. If it does not help then could you please send me your pdb file and I will try to sort out. Garib On 16 Mar 2009, at 22:43, 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/ 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 new Email address! Grab the Email name you#39;ve always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/
[ccp4bb] Error message while refining protein-DNA complex structure in Refmac5
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/
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 e_rajaku...@yahoo.com 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
