[ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units
Hello, everyone，o:p/o:pnbsp;Recently, we found an intermolecular disulfide bond from different symmetric units. I want to define it to refine, such as by refmac5. nbsp;I know the regular format of a disulfide bond in the same symmetric unit and show it as below.o:p/o:pnbsp;SSBONDnbsp;nbsp; 1 CYS Anbsp; 115nbsp;nbsp;nbsp; CYS Anbsp; 191o:p/o:pnbsp;My question is：nbsp;How to define a disulfide bond from different symmetric units?o:p/o:pnbsp;Best,o:p/o:pzhongzhou chen
Re: [ccp4bb] Interesting DNA contamination
Dear Stefan, just saw this after reading post: http://www.nature.com/nature/journal/v522/n7557/full/nature14559.html Best, Guenter Pramod, You already got good suggestions on how to handle DNA contamination in protein preparations. Let me point out briefly that you haven't demonstrated yet that your contamination is DNA. I had the same observation when purifying UvsX. A very persistent and strong contamination in all my preps at ~500kb. To test weather it was DNA or RNA I boiled the protein 30 minutes and incubated it with DNAase and RNAse and result was the same. I concluded it was neither RNA nor DNA and continued as if nothing had happened. This publication is reporting the same observation: Formosa and Alberts (1986) Purification and characterization of the T4 bacteriophage uvsX protein. J Biol Chem. 1986 May 5;261(13):6107-18. If you ever find out what it is that runs like 500kb DNA on Agarose, please let me know. S.
[ccp4bb] analysing conserved waters in two related structures
Can anyone suggest a method/program for analysing conserved waters between two related protein structures? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4614-3954-7
Re: [ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units
you add something like 2555 to define the required symmetry operator on the ssbond line. - the exact format is described in the pdb convention. But I think refmac does it i think if you as it to make disulphides. Eleanor On 28 June 2015 at 09:33, Zhongzhou Chen zhongzhouc...@sohu.com wrote: Hello, everyone， Recently, we found an intermolecular disulfide bond from different symmetric units. I want to define it to refine, such as by refmac5. I know the regular format of a disulfide bond in the same symmetric unit and show it as below. SSBOND 1 CYS A 115CYS A 191 My question is： How to define a disulfide bond from different symmetric units? Best, -- zhongzhou chen
Re: [ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units
Dear Prof. Eleanornbsp;Dodson,o:p/o:p o:pnbsp;/o:p nbsp;Thanks for your good suggestion.o:p/o:p It works for my pdb.o:p/o:p o:pnbsp;/o:p Best,o:p/o:pzhongzhougt;nbsp;you add something like 2555 to define the required symmetry operator on the ssbond line. - the exact format is described in the pdb convention.nbsp;But I think refmac does it i think if you as it to make disulphides.EleanorOn 28 June 2015 at 09:33, Zhongzhou Chenlt;zhongzhouc...@sohu.comgt;nbsp;wrote:Hello, everyone，nbsp;Recently, we found an intermolecular disulfide bond from different symmetric units. I want to define it to refine, such as by refmac5.nbsp; I know the regular format of a disulfide bond in the same symmetric unit and show it as below.nbsp;SSBONDnbsp;nbsp; 1 CYS Anbsp; 115nbsp;nbsp;nbsp; CYS Anbsp; 191nbsp;My question is：nbsp;How to define a disulfide bond from different symmetric units?nbsp;Best,zhongzhou chen
Re: [ccp4bb] imosflm errors
Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png
Re: [ccp4bb] imosflm errors
Thanks for your suggestion, Jurgen I tried xia2 and tried it several times, turning the machine off, rebooting, using different data sets, exiting ccp4i but every time it gives this error msg.(attached) On Sun, Jun 28, 2015 at 2:16 PM, Jurgen Bosch jbos...@jhu.edu wrote: Try xia2 from ccp4i and see if it also chokes. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 13:51, xaravich ivan xaravich.i...@gmail.com wrote: Thanks Jurgen, But there is no space in the last directory, I do not know where it is coming from. Its really making me crazy, because I have 0.95 Angs data of a long peptide, I wanted to solve it over the weekend!! I have no clue why this is happening Thanks for your suggestion! On Sun, Jun 28, 2015 at 9:51 AM, Jurgen Bosch jbos...@jhu.edu wrote: do you have a space in the last directory 1-03/103 1 ? That might be the reason it fails Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jun 28, 2015, at 12:47 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear ccp4 users, I am starting to solve a new structure after a long time and using my Mac for the first time. As all the data has been downloaded remotely into this mac, currently I am stuck using this machine. Now I am trying to upload my images into CCP4i mosflm and getting these errors.( attached screen shot) How do I fix this? Thanks in advance, ivan Screen Shot 2015-06-28 at 9.43.09 AM.pngScreen Shot 2015-06-28 at 9.42.16 AM.png
