Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
I have to withdraw what I stated in the post below. I forget and overlooked that we have bltwish installed together with ccp4i. I would like to apologise, Tim On Thu, Apr 15, 2010 at 08:20:13AM +0200, Tim Gruene wrote: Dear Bill, as I pointed out in my previous post I have the impression that using wish (instead of bltwish) libblt provided in Debian stable now works fine with ccp4, including loggraph etc. So it might be too late for a complaint, although my statement is based only on a first impression rather than an extensive test. Tim On Wed, Apr 14, 2010 at 07:58:50PM -0700, William G. Scott wrote: Yo Hari: The symbolic link won't solve the problem. I managed to scrape together a blt for tcltk 8.5 on OSX, so it is possible. Most of the hacks in turn came from a different Linux distro (gentoo) so it should be possible on ubuntu. Here by the way is the patch: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/unstable/main/finkinfo/x11/blt-x86_64.patch debian and ubuntu distribute blt without the bltwish executable, and I apparently put a huge weed up their arse a couple of years ago by reporting this as a bug. They are totally inflexible. Like IT support people, the maintainers think you work for them rather than vice versa. It might be worth flooding them with complaints and bug reports. Bill On Apr 14, 2010, at 7:49 AM, hari jayaram hari...@gmail.com wrote: Hi Tim, Thanks a tonne Tim for the pointer on how bltwish is handled in debian. A symlink from /usr/bin/wish to /usr/bin/bltwish. Seems to at-least start ccp4i. Now to see if it will also plot my graphs Hari -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] X-Ray films
I have a vague recollection of a student carrying books about crystallography getting beaten up at the start of Clockwork Orange. This might only be in the book though... This opens a whole new can of worms! How many films would contain references to crystallography if only the screenwriter hadn't decide to omit the reference in favour of something else more fun. Phil. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of harry powell Sent: Thursday, April 15, 2010 5:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-Ray films Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite movies involving real science, especially crystallography might be? If they're from Hollywood, though, I'd guess it should be favorite... I'm a little tired, but the only one I can think of at the moment is actually based on results from fibre diffraction - Life Story, with Jeff Goldblum. There must be others, though. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- DISCLAIMER: This e-mail and any attachments are confidential. They may contain privileged information and are intended for the named addressee(s) only. If you are not the named addressee do not disseminate, distribute, copy or retain this e-mail, or any part of it, in any manner. Please notify the sender immediately if you have received this e-mail by mistake and delete it from your system. The sender does not accept any liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. Unless expressly stated, opinions in this e-mail are those of the individual sender, and not of Galapagos NV or any of its subsidiaries including BioFocus. Galapagos NV and its subsidiaries including BioFocus reserve the right to monitor all e-mail communications through its network. Although this e-mail has been scanned for all known viruses, the sender does not guarantee that this message is virus-free and disclaims any liability for viruses that may be transmitted with this message.
Re: [ccp4bb] X-Ray films
All students (and professors) should see this too - I don't know whether it is a crystallography paper that is under consideration, but it shows the possible ultimate reward for your hard work. http://www.youtube.com/watch?v=-VRBWLpYCPY best wishes Pete Artymiuk P.S. German speakers will have to turn the sound right down to appreciate the English subtitles. On 16 Apr 2010, at 03:56, xaravich ivan wrote: Right you are, Chayne, I think it should be shown to every Protein crystallographer graduate student on their first day in the lab. ivan On Thu, Apr 15, 2010 at 11:42 AM, Chayne Piscitelli pisci...@ohsu.edu wrote: The documentary Naturally Obsessed: The Making of a Scientist is definitely a must-see film. It captures the story of life and science in a crystallography lab, that of Dr. Larry Shapiro at Columbia University, and follows the graduate students journey of fortune and misfortune that crystallographers know so well. Not to sound too sappy about it, but it is almost like a coming of age story for graduate students Check it out: http://naturallyobsessed.com/ -Chayne Piscitelli From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Brad Bennett [bradbennet...@gmail.com] Sent: Thursday, April 15, 2010 9:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-Ray films Hi Harry- X-ray crystallography played an integral part in discoveries made in Michael Crichton's Andromeda Strain. Mainly it was used to determine the elemental composition and arrangement of the capsid or shell that the foreign organism was found within. Best- Brad On Thu, Apr 15, 2010 at 12:16 PM, harry powell ha...@mrc-lmb.cam.ac.uk wrote: Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite movies involving real science, especially crystallography might be? If they're from Hollywood, though, I'd guess it should be favorite... I'm a little tired, but the only one I can think of at the moment is actually based on results from fibre diffraction - Life Story, with Jeff Goldblum. There must be others, though. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] N-terminal sequencing
Beyond these (posted three weeks ago), I don't know any. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15004.html I use Jeff Keen's service, which very reliable and adaptable. Andreas On 16/04/2010 9:23, F.Xavier Gomis-Rüth wrote: Dear CCP4ers, does anybody know of a company that accurately but affordably makes N-terminal sequencing ? Thanks a lot in advance to everybody. Best regards, Xavier -- -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] How to show bonds between ligands and metal which are around 1.8-2.0 Ao far away, in pymol..??
Hi! their is no connection between the metal and ligand in my pdb.. how can i generate bonds between them using pymol..?? by the way the distance between ligands and metal is 1.8-2.0 Ao...?? Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php
Re: [ccp4bb] Summary: Phasing statistics
Since it is suggested to run SHARP in order to obtain the phasing statistics, I take the liberty to provide a link where the expressions for relevant quantities are specified : http://www.globalphasing.com/pipermail/sharp-discuss/2003-March/001490.html As a general problem, all these statistical indicators were defined in the early days of protein crystallography, in the context of the Blow Crick (1959) framework (i.e. assuming error-free native measurements) using MIR data (i.e. essentially yielding unimodal phase probability distributions). The R-Cullis was initially defined for centric reflections only. Modern maximum-likelihood phasing methods have abandoned the Blow Crick concept of error-free native measurements and use a full 2-dimensional probability distribution for acentric structure factors on the complex plane. The methods are therefore capable of adequately dealing with highly bimodal probability distributions (e.g. SIR, SAD) and with data where there is no native (or otherwise special) data set (e.g. MAD). It is not entirely evident how the Blow Crick Phasing-Power, R-Cullis and FOM can be extended and generalized. The approach adopted in SHARP is described in the page whose link is given above. Concerning the FOM, it is not strictly true that the FOM, evaluated on a 2-dimensional probability distribution is equal to the cosine of the phase error., This is only the case if one assumes the native amplitude to be error-free. However, the cases discussed by Ian (bimodal distributions in SIR or SAD) will be correctly dealt with by SHARP. Things become also more tricky when computing and using Hendrickson-Lattman (1970) coefficients since, in the general case, these can not be calculated in a meaningful way for the native phase probability distribution (see the discussion in section 8 of Bricogne et al. (2003) [Acta Cryst D.59, 2023-2030]. This is a very important issue in connection with the subsequent use of density-modification techniques, but it is often overlooked. Marc Harmer, Nicholas wrote: Dear Colleagues, I am very grateful to everyone who contributed to the discussion regarding phasing statistics that I initiated. I certainly found it very informative. Below is a summary of the technical responses that I regarding this problem. 1) Use some of the statistics that SHELXD and SHELXE do provide (e.g. CC/CCfree for SHELXD, CCfree and connectivity for SHELXE). These could be compared to statistics produced for well determined structures (e.g. see Debreczeni et al. 2003 Acta Cryst. D., D59, 688-696). 2) Take the results from SHELX and put them into SHARP to generate the statistics. 3) Take the results from SHELX and put them into phaser_er, CRANK, or MLPHARE (perhaps with more difficulty) to generate the statistics. Thanks to Rick Lewis, Boaz Shaanan, Ed Lowe and Eleanor Dodson for suggestions. Cheers, Nic Harmer [For anyone interested, I took approaches 1 and 2. I got a good figures for phasing power from SHARP (somehow I failed to find the Rcullis, never mind), quoted the FOM at the end of SHELX, and the values for CC/CCfree from SHELXD, and the map contrast in the original and inverted hands from SHELXE. These all looked quite convincing, so hopefully my referees will be happy.] -- Marc SCHILTZ http://lcr.epfl.ch
Re: [ccp4bb] How to show bonds between ligands and metal which are around 1.8-2.0 Ao far away, in pymol..??
Hussain Bhukyagps wrote: Hi! their is no connection between the metal and ligand in my pdb.. how can i generate bonds between them using pymol..?? by the way the distance between ligands and metal is 1.8-2.0 Ao...?? Hussain Hi, What about specifying the bonds with CONECT records in the PDB file? From the PDB specs section: CONECT Overview The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB. Record Format COLUMNS DATA TYPEFIELD DEFINITION - 1 - 6 Record name CONECT 7 - 11 Integer serial Atom serial number 12 - 16 Integer serial Serial number of bonded atom 17 - 21 Integer serial Serial number of bonded atom 22 - 26 Integer serial Serial number of bonded atom 27 - 31 Integer serial Serial number of bonded atom 32 - 36 Integer serial Serial number of hydrogen bonded atom 37 - 41 Integer serial Serial number of hydrogen bonded atom 42 - 46 Integer serial Serial number of salt bridged atom 47 - 51 Integer serial Serial number of hydrogen bonded atom 52 - 56 Integer serial Serial number of hydrogen bonded atom 57 - 61 Integer serial Serial number of salt bridged atom Details * Intra-residue connectivity within non-standard (HET) residues (excluding water) is presented on the CONECT records. * Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups are represented on the CONECT records. * Disulfide bridges specified in the SSBOND records have corresponding CONECT records. * Hydrogen bonds and salt bridges have CONECT records. * No differentiation is made between donor and acceptor for hydrogen bonds. * No differentiation is made between atoms with excess negative or positive charge. * Atoms specified in the connectivity are presented by their serial numbers as found in the entry. * All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record. * If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used. * These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order. * The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11. * For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional. * For hydrogen bonds, when the hydrogen atom is present in the coordinates, PDB generates a CONECT record between the hydrogen atom and its acceptor atom. * For NMR entries, CONECT records for all models are generated describing heterogen connectivity and others for LINK records. Verification/Validation/Value Authority Control Connectivity is checked for unusual bond lengths. Relationships to Other Record Types CONECT records must be present in an entry that contains either non-standard groups or disulfide bonds. Example 1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 CONECT 1179 746 1184 1195 1203 CONECT 1179 1211 1222 CONECT 1021 544 1017 1020 1022 1211 1222 1311 Known Problems Only five digits are available for the atom serial number, but some structures have already been received with more that 99,999 atoms. Changing the field length would make earlier entries incorrect. CONECTs to atoms whose coordinates are not in the entry (e.g., symmetry-generated) are not given.
[ccp4bb] Entering mosflm keywords in imosflm 1.0.4
Hi I know there is (or certainly used to be in previous versions) a way to enter mosflm keywords from the imosflm gui (something like going to the log file in the history tab and hitting a certain key) but I can't remember what it was and google is finding me nothing other than: For expert users, iMosflm now has the option of specifying ipmosflm keywords for the very specialised options that are only rarely used and are not yet included in the iMosflm GUI explicitly. but not the details of how to do it! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] Entering mosflm keywords in imosflm 1.0.4
Hi again, I have just remembered what the magic keystroke combination was. I assume there is a reason this feature is undocumented so I'd better not post it Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] N-terminal sequencing
Just one more, which we are now using.. The protein analysis facility at University of Giessen offers a range of services to academic and non-academic customers: http://www.uni-giessen.de/cms/fbz/fb11/institute/biochemie/forschung/protein-analytik/gebuhrenubersicht-und-anforderungsformulare They offer good rates for academic customers and we are pleased with our first results. All the best, Tim -Original Message- From: CCP4 bulletin board on behalf of Andreas Förster Sent: Fri 16.04.2010 11:25 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] N-terminal sequencing Beyond these (posted three weeks ago), I don't know any. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15004.html I use Jeff Keen's service, which very reliable and adaptable. Andreas On 16/04/2010 9:23, F.Xavier Gomis-Rüth wrote: Dear CCP4ers, does anybody know of a company that accurately but affordably makes N-terminal sequencing ? Thanks a lot in advance to everybody. Best regards, Xavier -- -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] X-Ray films
You are absolutely right, it was not a student but an elderly scholar, probably professor of crystallography in one of the London colleges or Universities. Maybe Imperial (so we can also trace this person). Anthony Burgess, the author, probably projected someone he knew into the book. In the movie there is a scene of Alex's gang beating an elderly scholar, but the list of books that were in his possession is not there. I think it is still counts. I whatched the film after I have reading the book, and knew that crystallography book is there. ;--) Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Apr 16, 2010, at 11:33 , Philip Leonard wrote: I have a vague recollection of a student carrying books about crystallography getting beaten up at the start of Clockwork Orange. This might only be in the book though... This opens a whole new can of worms! How many films would contain references to crystallography if only the screenwriter hadn't decide to omit the reference in favour of something else more fun. Phil. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of harry powell Sent: Thursday, April 15, 2010 5:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-Ray films Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite movies involving real science, especially crystallography might be? If they're from Hollywood, though, I'd guess it should be favorite... I'm a little tired, but the only one I can think of at the moment is actually based on results from fibre diffraction - Life Story, with Jeff Goldblum. There must be others, though. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- DISCLAIMER: This e-mail and any attachments are confidential. They may contain privileged information and are intended for the named addressee(s) only. If you are not the named addressee do not disseminate, distribute, copy or retain this e-mail, or any part of it, in any manner. Please notify the sender immediately if you have received this e-mail by mistake and delete it from your system. The sender does not accept any liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. Unless expressly stated, opinions in this e-mail are those of the individual sender, and not of Galapagos NV or any of its subsidiaries including BioFocus. Galapagos NV and its subsidiaries including BioFocus reserve the right to monitor all e-mail communications through its network. Although this e-mail has been scanned for all known viruses, the sender does not guarantee that this message is virus-free and disclaims any liability for viruses that may be transmitted with this message.
Re: [ccp4bb] Entering mosflm keywords in imosflm 1.0.4
The required keystrokes are described (although somewhat hidden) under the heading What's new in version 1.0.0 in the imosflm web page. (www.mrc-lmb.cam.ac.uk/harry/imosflm/ver104) . There are good reasons for this option not being well advertised. One is that if keywords entered in this way set parameters that can also be set via the Experiment Settings or Processiong Options menus, the value set by the keyword will be overwritten and have no effect. Another is that we would like users to tell us which additional parameters they would like to be able to set (via the menus mentioned) so that we can assign priorities. Allowing all possible keyword options would make these menus unreasonably complicated which defeats one of the design goals for the interface. Andrew and Harry On 16 Apr 2010, at 11:23, Huw Jenkins wrote: Hi again, I have just remembered what the magic keystroke combination was. I assume there is a reason this feature is undocumented so I'd better not post it Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] How to show bonds between ligands and metal which are around 1.8-2.0 Ao far away, in pymol..??
On Fri, 16 Apr 2010 14:31:02 +0530, Hussain Bhukyagps wrote: Hi! their is no connection between the metal and ligand in my pdb.. how can i generate bonds between them using pymol..?? by the way the distance between ligands and metal is 1.8-2.0 Ao...?? Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- ** Blow, blow, thou winter wind Thou art not so unkind As man's ingratitude; Thy tooth is not so keen, Because thou art not seen, Although thy breath be rude. -William Shakespeare **
Re: [ccp4bb] How to show bonds between ligands and metal which are around 1.8-2.0 Ao far away, in pymol..??
I am sorry for sending that blank email earlier. Hussain, A good way to do that is to use the pymol distance measuring wizard. It draws a dotted line between the atoms, and writes out the distance in numbers. You can hide the numbers and leave the dotted line behind. ganesh On Fri, 16 Apr 2010 14:50:41 +0530, Hussain Bhukyagps wrote: Hi! their is no connection between the metal and ligand in my pdb.. how can i generate bonds between them using pymol..?? by the way the distance between ligands and metal is 1.8-2.0 Ao...?? Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- ** Blow, blow, thou winter wind Thou art not so unkind As man's ingratitude; Thy tooth is not so keen, Because thou art not seen, Although thy breath be rude. -William Shakespeare **
[ccp4bb] Scientific Programmer Position at the Nucleic Acid Database
Scientific Programmer Position at the Nucleic Acid Database The Nucleic Acid Database project at Rutgers University is seeking candidates for a scientific programmer position to support development of new tools and database services for macromolecular structure analysis. An ideal candidate should have an advanced degree in structural biology or computational chemistry and strong programming skills. Demonstrated experience with the following is highly desirable: proficiency in programming languages C++,and Python, design and development of large software application systems; webuser interface development using Java, web service development using SOAP and REST; database application development using JDBC and MySQL. The position holder should be able collaborate with broad, multidisciplinary teams. Excellent written and verbal communication skills are essential. Please respond to: j...@rcsb.rutgers.edu.
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Hello ,
I applied a few of the patches that Bill Scott suggested ( esp this blt
x86_64
patchhttp://fink.cvs.sourceforge.net/viewvc/*checkout*/fink/dists/10.4/unstable/main/finkinfo/x11/blt-x86_64.patch?revision=1.1)
and compiled blt2.4z , x86_64 (amd64) with Tcl 8.5 and Tk 8.5. ( gcc version
gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3)
Although the compilation proceeded ( with a modification of the Makefile
-diff below) without any glitches
ccp4i failed to launch with the errors given below.
For some reason gcc 4.4.3 or make didnt support the --compatibilty_version
and --current_version flags.
I did manage to use a gcc 4.2.4 compiled binary from another amd64 machine
on this machine .
Thanks for your help
Hari
###
ccp4i startup erros
###
Application initialization failed: invalid command name tcl_findLibrary
Top level CCP4 directory is /home/hari/ccp4src-try/ccp4-6.1.3
Using CCP4 programs from /home/hari/ccp4src-try/ccp4-6.1.3/bin
Error in startup script: invalid command name ::tcl::tm::UnknownHandler
while executing
::tcl::tm::UnknownHandler ::tclPkgUnknown msgcat 1.4
(package unknown script)
invoked from within
package require msgcat 1.4
(uplevel body line 2)
invoked from within
uplevel \#0 {
package require msgcat 1.4
if { $::tcl_platform(platform) eq {windows} } {
if { [catch { package require registry 1.1 }] } {
...
(file /usr/lib/tcl8.5/clock.tcl line 23)
invoked from within
source -encoding utf-8 [file join $TclLibDir clock.tcl]
(procedure ::tcl::clock::format line 3)
invoked from within
clock format $secs -format %d %b %Y %H:%M:%S
(procedure GetDate line 43)
invoked from within
GetDate
(procedure CreateSessionLog line 12)
invoked from within
CreateSessionLog
(procedure taskbrowser line 30)
invoked from within
$system(RUN_MODE)
(default arm line 9)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file
source [file join $env(CCP4I_...
(file /home/hari/ccp4src-try/ccp4-6.1.3/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /home/hari/ccp4src-try/ccp4-6.1.3/ccp4i/bin/ccp4i line 5)
Makefile modifications to get blt2.4z to compile on gcc 4.4.3
diff --git a/src/shared/Makefile b/src/shared/Makefile
index 78153cb..aec1d1c 100644
--- a/src/shared/Makefile
+++ b/src/shared/Makefile
@@ -145,14 +145,14 @@ $(lib_so): $(OBJS)
$(CC) -c $(CC_SWITCHES) -DBLT_LIBRARY=\$(scriptdir)\ \
$(srcdir)/bltInit.c
$(RM) $@
- $(SHLIB_LD) $(SHLIB_LD_FLAGS) -o $@ -install_name $(libdir)/$@
-compatibility_version 2.0 -current_version 2.4 bltInit.o $(OBJS) \
+ $(SHLIB_LD) $(SHLIB_LD_FLAGS) -o $@ -install_name $(libdir)/$@
bltInit.o $(OBJS) \
$(SHLIB_LIB_SPECS) $(LIBS)
$(tcl_only_lib_so): $(TCL_ONLY_OBJS)
$(CC) -c $(CC_SWITCHES) -DTCL_ONLY -DBLT_LIBRARY=\$(scriptdir)\ \
$(srcdir)/bltInit.c
$(RM) $@
- $(SHLIB_LD) $(SHLIB_LD_FLAGS) -o $@ -install_name $(libdir)/$@
-compatibility_version 2.0 -current_version 2.4 bltInit.o
$(TCL_ONLY_OBJS) \
+ $(SHLIB_LD) $(SHLIB_LD_FLAGS) -o $@ -install_name $(libdir)/$@
bltInit.o $(TCL_ONLY_OBJS) \
$(SHLIB_TCL_ONLY_LIB_SPECS) $(TCL_ONLY_LIB_SPECS)
Thanks
Hari
On Fri, Apr 16, 2010 at 2:47 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
I have to withdraw what I stated in the post below. I forget and
overlooked that
we have bltwish installed together with ccp4i.
I would like to apologise, Tim
On Thu, Apr 15, 2010 at 08:20:13AM +0200, Tim Gruene wrote:
Dear Bill,
as I pointed out in my previous post I have the impression that using
wish
(instead of bltwish) libblt provided in Debian stable now works fine with
ccp4,
including loggraph etc.
So it might be too late for a complaint, although my statement is based
only on
a first impression rather than an extensive test.
Tim
On Wed, Apr 14, 2010 at 07:58:50PM -0700, William G. Scott wrote:
Yo Hari:
The symbolic link won't solve the problem.
I managed to scrape together a blt for tcltk 8.5 on OSX, so it is
possible. Most of the hacks in turn came from a different Linux distro
(gentoo) so it should be possible on ubuntu.
Here by the way is the patch:
http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/unstable/main/finkinfo/x11/blt-x86_64.patch
debian and ubuntu distribute blt without the bltwish executable, and I
apparently put a huge weed up their arse a couple of years ago by reporting
this as a bug. They are totally inflexible. Like IT support people, the
maintainers think you work for them rather than vice versa. It might be
worth flooding them with complaints and bug reports.
Bill
On Apr 14, 2010, at
Re: [ccp4bb] How to show bonds between ligands and metal which are around 1.8-2.0 Ao far away, in pymol..??
Use bond command bond atom1, atom2 once you do that, any subsequent line and stick renderings will connect the atom1 and atom2 (you can right-click on the corresponding atom to see their full string representation). I assume you are trying to do something like this http://tinyurl.com/y2cdezj In this figure, metal ion was connected to its ligands by lines, not sticks. Lines become thicker once you do ray-tracing. If you want to remove the connection, use the unbond command on the same atoms. HTH, Ed. On Fri, 2010-04-16 at 14:31 +0530, Hussain Bhukyagps wrote: Hi! their is no connection between the metal and ligand in my pdb.. how can i generate bonds between them using pymol..?? by the way the distance between ligands and metal is 1.8-2.0 Ao...?? Hussain Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] Proportion of MOLECULAR REPLACEMENT in PDB
According to Nicholas keep n.k...@mail.cryst.bbk.ac.uk: Does anyone have a good estimate of the proportion of molecular replacement structures in the PDB? This is what OCA has: From un total of 64,623 PDB structure files, 30,784 have 'MOLECULAR REPLACEMENT' as Method for Structure Determination. However, you must remember that we have a large number of false negatives Several reasons: - Only 47,557 structure files from the total of 64,623 report which method was used for structure determination. For example, 1CRY whose title reports using the MR method does not include the info in the proper REMARK. - Users are allowed to write almost anything as the METHOD USED TO DETERMINE THE STRUCTURE, making it difficult an accurate report. OCA found PDB italian speaking structure files reporting 'MOLECULARE REPLACEMENT' ... This and other problems are being reported to RCSB. OCA makes public some of its internal statistics on PDB, like http://oca.weizmann.ac.il/oca-docs/PDBSizeDistribution.html, http://bip.weizmann.ac.il/oca-bin/pdbRecNames and http://proteopedia.org/wiki/index.php/Believe_It_or_Not Regards, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D)
Re: [ccp4bb] X-Ray films
On Apr 16, 2010, at 5:15 AM, Judith Murray-Rust wrote: The list of books is here. http://kubrickmovies.hostei.com/aconovel.html Dim and Pete doing a tug-of-war with The Rhombohedral System. The starry prof type began to creech: 'But those are not mine, those are the property of the municipality, this is sheer wantonness and vandal work,' or some such slovos. And he tried to sort of wrest the books back off of us, which was like pathetic. 'You deserve to be taught a lesson, brother,' I said, 'that you do.' This crystal book I had was very tough-bound and hard to razrez to bits, being real starry and made in days when things were made to last like, but I managed to rip the pages up and chuck them in handfuls of like snowflakes, though big, all over this creeching old veck, and then the others did the same with theirs, old Dim just dancing about like the clown he was.
Re: [ccp4bb] X-Ray films
Well, I have to admit that that whole R32 vs H32 thing bugs me too ... James Stroud wrote: On Apr 16, 2010, at 5:15 AM, Judith Murray-Rust wrote: The list of books is here. http://kubrickmovies.hostei.com/aconovel.html Dim and Pete doing a tug-of-war with /The Rhombohedral System/. The starry prof type began to creech: 'But those are not mine, those are the property of the municipality, this is sheer wantonness and vandal work,' or some such slovos. And he tried to sort of wrest the books back off of us, which was like pathetic. 'You deserve to be taught a lesson, brother,' I said, 'that you do.' This crystal book I had was very tough-bound and hard to razrez to bits, being real starry and made in days when things were made to last like, but I managed to rip the pages up and chuck them in handfuls of like snowflakes, though big, all over this creeching old veck, and then the others did the same with theirs, old Dim just dancing about like the clown he was.
Re: [ccp4bb] X-Ray films and BOOKS
I would also suggest CP Snow, The search, written in 1934 Very crystallographic, very touching, probably inspired by CP Snow friend JD Bernal This is about our life, friends... FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Apr 16, 2010, at 21:38 , James Holton wrote: Well, I have to admit that that whole R32 vs H32 thing bugs me too ... James Stroud wrote: On Apr 16, 2010, at 5:15 AM, Judith Murray-Rust wrote: The list of books is here. http://kubrickmovies.hostei.com/aconovel.html Dim and Pete doing a tug-of-war with /The Rhombohedral System/. The starry prof type began to creech: 'But those are not mine, those are the property of the municipality, this is sheer wantonness and vandal work,' or some such slovos. And he tried to sort of wrest the books back off of us, which was like pathetic. 'You deserve to be taught a lesson, brother,' I said, 'that you do.' This crystal book I had was very tough-bound and hard to razrez to bits, being real starry and made in days when things were made to last like, but I managed to rip the pages up and chuck them in handfuls of like snowflakes, though big, all over this creeching old veck, and then the others did the same with theirs, old Dim just dancing about like the clown he was.
[ccp4bb] Arp Waters vs coot find waters!
Hi everyone, I am in the process of refining my structure. I have built almost the whole protein. Now its time to add waters. Should I do refinement in refmac5 with (adding waters running coot) or should I use Arp/wArp waters or both?. I have 2.15 Angs near data and about 1200 residues. Does it matter which program I use to add water? Is there something specific I should look for? I apologise in advance if this question has already been asked before. Thanks, Ivan
