Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?
Dear Bill, Yes, the same happened a year ago or so to me, with a 17 inch MacBookPro bought in 2008. The Apple store in Glasgow replaced it for free within roughly one week, and the laptop works well. I agree that this is really dangerous, I wonder if it could also cause the leak of material from inside (mine exposed some really ugly brown stuff). Laura On Nov 18, 2012, at 12:28 AM, William G. Scott wrote: Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: CIMG4451.jpeg That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA Dr Laura Spagnolo Institute of Structural Molecular Biology University of Edinburgh Room 506, Darwin Building King's Buildings Campus Edinburgh EH9 3JR United Kingdom T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo laura.spagn...@ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
In Coot: Centre on the atom/place of interest. Extensions-Modelling-New Molecule by Sphere then select the molecule and sphere radius. B I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - No virus found in this message. Checked by AVG - www.avg.com Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Hi Pavel, does this also work for symmetry related atoms ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 14:26, Pavel Afonine pafon...@gmail.commailto:pafon...@gmail.com wrote: Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and name CA) --write-pdb-file=cut.pdb which in the above example selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. Pavel On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer rex.pal...@btinternet.commailto:rex.pal...@btinternet.com wrote: I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
In O, the command is called symm_sphere. http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_s.html#anchor536668 James On Nov 18, 2012, at 10:14 AM, Bosch, Juergen wrote: Hi Pavel, does this also work for symmetry related atoms ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 14:26, Pavel Afonine pafon...@gmail.com wrote: Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and name CA) --write-pdb-file=cut.pdb which in the above example selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. Pavel On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer rex.pal...@btinternet.com wrote: I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?
Bill I think that's crap. I had issues on a 2005 MacBook Pro with inflating battery and it was replaced (after about 6 months). There were troubles with those batteries and impurities but mine still had apple care at that time and the batteries were exchangeable. I have not heard of the build in batteries to have problems but yours sure did. Send Tim Cook an email with the picture. This should not have happened and also keeping the power cord on leading to this problem should not have happened. For what did they introduce the trickling charging ? If you can't leave the coord plugged in how many nice wooden US households gave caught fire due to Apple products ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 16:28, William G. Scott wgsc...@ucsc.edu wrote: Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: CIMG4451.jpeg That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Of course (sort of): Extensions-Maps-Export Local Map Fragment B This is nice. Can it do the same for the map? Thanks Jim Brannigan On 18 November 2012 15:52, Bernhard C. Lohkamp bernh...@chem.gla.ac.ukwrote: In Coot: Centre on the atom/place of interest. Extensions-Modelling-New Molecule by Sphere then select the molecule and sphere radius. B I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/**our-staff/emeritus-staffhttp://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.**homestead.com http://rexpalmer2010.homestead.com - No virus found in this message. Checked by AVG - www.avg.com Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12 - No virus found in this message. Checked by AVG - www.avg.com Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
On 11/17/2012 03:04 PM, Rex Palmer wrote:
I would like to specify a target atom in a pdb file and then isolate
all atoms within a given distance of the target. The selected atoms
are then to be placed in a new pdb file.
AWKward BASHing:
#! /bin/bash
read x y z $(awk '{if(substr($0,1,4)==ATOM
int(substr($0,7,5))==75) print
substr($0,31,8),substr($0,39,8),substr($0,47,8);}' model.pdb)
awk -v x=$x -v y=$y -v z=$z '{if(substr($0,1,4)==ATOM
sqrt((substr($0,31,8)-x)^2+(substr($0,39,8)-y)^2+(substr($0,47,8)-z)^2)4.0)
print;}' model.pdb out.pdb
You did not specify your atom selection criteria, so I simply use the
atom serial number. To make it more flexible so that it takes model pdb
file name, atom serial number for selection, distance cutoff and output
file name, this should work
#! /bin/bash
read x y z $(awk -v num=$2 '{if(substr($0,1,4)==ATOM
int(substr($0,7,5))==num) print
substr($0,31,8),substr($0,39,8),substr($0,47,8);}' $1)
awk -v cutoff=$3 -v x=$x -v y=$y -v z=$z '{if(substr($0,1,4)==ATOM
sqrt((substr($0,31,8)-x)^2+(substr($0,39,8)-y)^2+(substr($0,47,8)-z)^2)cutoff)
print;}' $1 $4
It takes about 27ms on a ~3000 atom model (core i7 2600K@3.4GHz, running
precise pangolin). It's not hard to modify the atom selection, if
necessary. I wonder if this is, surprisingly, much faster than all
other options that rely on external programs. For example, it takes
over 120ms just to open and close pymol in batch mode, over 2 seconds
for coot. phenix.pdb_atom_selection takes about 2.5s.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
Re: [ccp4bb] CCP4BB Digest - 17 Nov 2012 to 18 Nov 2012 (#2012-327)
I had exactly the same thing happen this year to a 2008 macbook pro. Computer still worked while attached to power but unsurprisingly the battery did not work after that. On Nov 18, 2012, at 7:00 PM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: There are 8 messages totaling 1223 lines in this issue. Topics of the day: 1. OT: Has anyone experienced problems with Apple laptop battery expansion? (3) 2. Off topic: Selecting atoms within a given distance from a target atom (5) -- Date:Sat, 17 Nov 2012 16:28:07 -0800 From:William G. Scott wgsc...@ucsc.edu Subject: OT: Has anyone experienced problems with Apple laptop battery expansion? Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA -- Date:Sun, 18 Nov 2012 08:01:37 + From:Laura Spagnolo laura.spagn...@ed.ac.uk Subject: Re: OT: Has anyone experienced problems with Apple laptop battery expansion? Dear Bill, Yes, the same happened a year ago or so to me, with a 17 inch MacBookPro bought in 2008. The Apple store in Glasgow replaced it for free within roughly one week, and the laptop works well. I agree that this is really dangerous, I wonder if it could also cause the leak of material from inside (mine exposed some really ugly brown stuff). Laura On Nov 18, 2012, at 12:28 AM, William G. Scott wrote: Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: CIMG4451.jpeg That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA Dr Laura Spagnolo Institute of Structural Molecular Biology University of Edinburgh Room 506, Darwin Building King's Buildings Campus Edinburgh EH9 3JR United Kingdom T: +44 (0)131 650 7066 F: +44 (0)131 650 8650 http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo laura.spagn...@ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Date:Sun, 18 Nov 2012 16:52:08 +0100 From:Bernhard C. Lohkamp bernh...@chem.gla.ac.uk Subject: Re: Off topic: Selecting atoms within a given distance from a target atom In Coot: Centre on the atom/place of interest. Extensions-Modelling-New Molecule by Sphere then select the molecule and sphere radius. B I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - No virus found in this message. Checked by AVG - www.avg.com Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12 -- Date:Sun, 18 Nov 2012 12:14:43 -0500 From:Bosch, Juergen jubo...@jhsph.edu Subject: Re: Off topic: Selecting atoms within a given distance from a target atom Hi Pavel, does this also work for symmetry related atoms ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 14:26, Pavel Afonine pafon...@gmail.commailto:pafon...@gmail.com wrote: Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and name CA)
Re: [ccp4bb] hkl2000 install
OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] hkl2000 install
Not sure it is what you need. I put an external screen to my laptop when I use HKL2000 for remote collection. Best, Nian Huang, Ph.D. On Sun, Nov 18, 2012 at 8:48 PM, 王瑞 wangrui...@gmail.com wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] hkl2000 install
a. What operation system your notebook is running? b. There is no version of HKL2000 for Windows. c. Move to 17 laptop with larger resolution d. You will need special HKL2000 licence for the laptop FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 19, 2012, at 03:48 , 王瑞 wangrui...@gmail.com wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Hi Jürgen, it should properly take symmetry into account. I would be very surprised if it doesn't. Pavel On Sun, Nov 18, 2012 at 9:14 AM, Bosch, Juergen jubo...@jhsph.edu wrote: Hi Pavel, does this also work for symmetry related atoms ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 14:26, Pavel Afonine pafon...@gmail.com wrote: Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and name CA) --write-pdb-file=cut.pdb which in the above example selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. Pavel On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer rex.pal...@btinternet.comwrote: I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] hkl2000 install
Make your life easier and use CCP4's imosflm (this is the CCP4 bb after all) On Nov 18, 2012, at 5:48 PM, 王瑞 wangrui...@gmail.com wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
[ccp4bb] Temperature and crystallization
Dear All, Will you please give a comment on how the temperature influences on the possibility to get protein crystal, and how the temperatures used to get the protein crystals of the same protein influences the protein 3-D structures of the same protein got based on the crystals of the same protein got at different temperatures? Cheers, Acoot
