Re: [ccp4bb] generating separate pdb files
Hi Charlie,
This may not be what you want, but this perl script seemed to work just now on
1g9e.pdb
$base='1g9e';open(IN,$base.pdb);@indata = IN;$i=0;
foreach $line(@indata) {
if($line =~ /^MODEL/) {++$i;$file=${base}_$i.pdb;open(OUT,$file);next}
if($line =~ /^ENDMDL/) {next}
if($line =~ /^ATOM/ || $line =~ /^HETATM/) {print OUT $line}
}
Hope it helps you,
Mike
[ccp4bb] pdb formats
Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College
Re: [ccp4bb] pdb formats
Dear Rex, could you give us an example of a non-old version of the PDB format? In all PDB files I have seen, each atom occupied its own line, and I am not aware of any recent changes of the PDB. Cheers, Tim On Tue, Dec 14, 2010 at 11:34:11AM +, REX PALMER wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] pdb formats
Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College
Re: [ccp4bb] pdb formats
Why, by the way, is the default text editor in windows, notepad, such a lousy text editor? (Sounds like a riddle, I guess, but is really a question...) JPK On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote: Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] pdb formats
It trains you to only use files created by MS Windows and complain if you get files that use another standard. As usual, follow the money... On Tue, Dec 14, 2010 at 14:45, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Why, by the way, is the default text editor in windows, notepad, such a lousy text editor? (Sounds like a riddle, I guess, but is really a question...) JPK On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote: Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] generating separate pdb files
On Tue, 2010-12-14 at 08:02 +0100, Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb files
from a long file with multiple (100) models. My file does not contain
separate chain IDs, so I cannot use moleman2 or splitpdb.p. I want to retain
information about ligands, and so do not want to use drussel's program. CCP4
appears not to offer such capability. Anyone know how to do this?
Thanks,
Charlie
I assume that you have an NMR-style file where individual models are
correctly separated by MODEL/ENDMDL records. Let me know if it's
something else and I'll come up with a different one-liner
grep -n 'MODEL\|ENDMDL' models.pdb | cut -d: -f 1 | awk '{if(NR%2)
printf sed -n %d,,$1+1; else printf %dp model_%03d.pdb\n,
$1-1,NR/2;}' | bash -sf
You multi-model file is models.pdb and it will be split into individual
files named model_###.pdb.
Cheers,
Ed.
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
Re: [ccp4bb] pdb formats
I use NoteTabLight, which seems to work pretty well. JPK On Tue, Dec 14, 2010 at 11:05 AM, Kelly Daughtry kddau...@bu.edu wrote: Notepad++ is a free windows text editor that recognizes the line breaks, and does a multitude of other functions. http://notepad-plus-plus.org/ Best, Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *** On Tue, Dec 14, 2010 at 9:01 AM, Thomas Juettemann juettem...@gmail.com wrote: It trains you to only use files created by MS Windows and complain if you get files that use another standard. As usual, follow the money... On Tue, Dec 14, 2010 at 14:45, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Why, by the way, is the default text editor in windows, notepad, such a lousy text editor? (Sounds like a riddle, I guess, but is really a question...) JPK On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote: Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] cmakereference : reading reflections
does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset' or 'crystal' to be in the .mtz? because i thought by default, these were eponymous e.g my .mtz - that has labels F and sigF - : * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 project crystal dataset ... because i am stuck this error : CCP4MTZfile: import_hkl_data - Missing column, crystal or dataset: NONE.F_sigF.F terminate called after throwing an instance of 'clipper::Message_fatal' ... if the labels are not F or sigF the same error occurs. -Bryan
[ccp4bb] Postdoctoral Position: Membrane Protein Structural Genomics
Postdoctoral Position: Membrane Protein Structural Genomics A postdoctoral position is available immediately (!) in the laboratory of Michael Wiener, University of Virginia. His lab is one of three that comprise the Membrane Protein Structural Biology Consortium (MPSBC, http://mpsbc.org, one of nine groups recently funded as part of the NIH PSI:Biology Network. The other labs are those of Mark Dumont (University of Rochester) and Michael Malkowski (Hauptman-Woodward Medical Research Institute). The primary targets of MPSBC are eukaryotic integral membrane proteins (transporters, enzymes, channels). Experience in one or more of the following is required: protein expression purification (including upstream molecular biology), crystallization and crystallography. Experience with the insect cell baculovirus expresson system is especially desirable. This is an excellent opportunity to be part of a multi-lab effort to determine eukaryotic membrane protein structures, and to develop technologies (such as pre-crystallization screening) fo r improvement of throughput. The scientific and intellectual environment for membrane research is strong at the University of Virginia. Eight labs working in membrane protein biochemistry, biophysics and structural biology are sited in a modern research building. The Center for Membrane Biology includes additional investigators, holds a regular seminar series, and maintains a collaborative and collegial environment. Applicants, please send a cover letter, cv, names of three references, and any other queries to Michael Wiener, mwie...@virginia.edu, 434-243-2731. Please indicate that you are applying for the Structural Genomics position. [The University of Virginia is an Equal Opportunity/Affirmative Action Employer.]
[ccp4bb] Postdoctoral Position: Structural Biology of Bacterial Active Transport
Postdoctoral Position: Structural Biology of Bacterial Active Transport A postdoctoral position is available immediately (!) in the laboratory of Michael Wiener, University of Virginia. The laboratory has a long-running program in structural and functional studies of TonB-dependent outer membrane active transport (relevant structures from the lab include 1NQE and 2GSK). Experience in one or more of the following is required: bacterial protein expression purification, bacteriology (functional in vivo studies), biochemical methods, crystallization and crystallography. This is an excellent opportunity for someone who is interested in creatively combining structural and functional approaches to elucidate molecular mechanism. The scientific and intellectual environment for membrane research is strong at the University of Virginia. Eight labs working in membrane protein biochemistry, biophysics and structural biology are sited in a modern research building. The Center for Membrane Biology includes additional investigators, holds a regular seminar series, and maintains a collaborative and collegial environment. Applicants, please send a cover letter, cv, names of three references, and any other queries to Michael Wiener, mwie...@virginia.edu, 434-243-2731. Please indicate that you are applying for the Membrane Transport position. [The University of Virginia is an Equal Opportunity/Affirmative Action Employer.]
Re: [ccp4bb] pdb formats
On Tuesday, December 14, 2010 09:05:04 am Kelly Daughtry wrote: Notepad++ is a free windows text editor that recognizes the line breaks, and does a multitude of other functions. http://notepad-plus-plus.org/ It's not relevant to editing PDB files, but be warned that neither notepad nor notepad++ is compatible with unix/linux files that use UTF-8 encoding. [I recently wasted a chunk of time figuring out that this was the underlying cause for a bug report on one of my programs] cheers, Ethan http://notepad-plus-plus.org/Best, Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *** On Tue, Dec 14, 2010 at 9:01 AM, Thomas Juettemann juettem...@gmail.comwrote: It trains you to only use files created by MS Windows and complain if you get files that use another standard. As usual, follow the money... On Tue, Dec 14, 2010 at 14:45, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Why, by the way, is the default text editor in windows, notepad, such a lousy text editor? (Sounds like a riddle, I guess, but is really a question...) JPK On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote: Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] cns .map in coot
Hi all, I can easily convert my composite omit map from cns to ccp4 format and open it into coot. However, how can I make coot use this map to fit density to my structure ? I can only use this map for visual support and for example, coot doesn't assign any density on the bar graph generated by using the Density fit analysis option to check the geometry. Does anyone have any idea how to fix this problem? Thanks, Julian
[ccp4bb] Research Associate position at Vanderbilt University
Dear All An opening is available in the laboratory of Dr. Stephen Fesik (http://www.mc.vanderbilt.edu/root/vumc.php?site=fesiklab) for a research associate. The position requires a B.S. or M.S. degree in biochemistry or a related field with 1-2 years of experience in a research laboratory performing basic laboratory functions such as making buffers, media and handling basic lab equipments such as fermentor, centrifuges, shakers, and UV/VIS spectrophotometer; experience with standard curve analysis, SDS PAGE, bacterial culture, and protein purification by FPLC is preferred; experience in protein crystallization is highly preferred. The ideal candidate should be courteous, responsible, organized, hard-working, and be able to multi-task and communicate efficiently. The successful candidate will be trained initially but will work independently or with limited supervision on assigned duties thereafter. Please send CV or resume to jason.p...@vanderbilt.edu Thanks, Jason
Re: [ccp4bb] cns .map in coot
You should have also gotten the .coeff file - try converting it to mtz and using with coot. On Tue, 2010-12-14 at 14:01 -0600, Julian Nomme wrote: Hi all, I can easily convert my composite omit map from cns to ccp4 format and open it into coot. However, how can I make coot use this map to fit density to my structure ? I can only use this map for visual support and for example, coot doesn't assign any density on the bar graph generated by using the Density fit analysis option to check the geometry. Does anyone have any idea how to fix this problem? Thanks, Julian -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] generating separate pdb files
Well it's not as impressive as some solutions posted, but three lines of awk
will
do the job too. Search for END or ENDMDL as you wish.
BEGIN {file = 0; filename = charlie_ file .pdb}
/ENDMDL/ {getline; file ++; filename = charlie_ file .pdb}
{print $0 filename}
Call this script charlie.awk and then try
awk -f charlie.awk 1G9E.pdb
cheers
Jeremy
On Dec 14, 2010, at 4:02 PM, Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb files
from a long file with multiple (100) models. My file does not contain
separate chain IDs, so I cannot use moleman2 or splitpdb.p. I want to retain
information about ligands, and so do not want to use drussel's program. CCP4
appears not to offer such capability. Anyone know how to do this?
Thanks,
Charlie
Re: [ccp4bb] generating separate pdb files
On 08:02 Tue 14 Dec , Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb
files from a long file with multiple (100) models. My file does not
contain separate chain IDs, so I cannot use moleman2 or splitpdb.p. I
want to retain information about ligands, and so do not want to use
drussel's program. CCP4 appears not to offer such capability. Anyone
know how to do this?
Yet another solution, this time in bash (again assuming ENDMDL exists):
i=1
while read -a line; do
echo ${li...@]} model_${i}.pdb
[[ ${line[0]} == ENDMDL ]] ((i++))
done /path/to/file.pdb
--
Thanks,
Donnie
Donald S. Berkholz, Ph.D.
Research Fellow
James R. Thompson lab, Physiology Biomedical Engineering
Grazia Isaya lab, Pediatric Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905
office: 507-538-6924
cell: 612-991-1321
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