Re: [ccp4bb] BLT wish
Hi Bill Sorry, I was tired! Yes, I agree entirely. Trying to maintain one's own working TclTk from source is not straightforward, and best avoided. CCP4 know this and are working hard to remedy the situation! On 17 Aug 2011, at 23:31, William Scott wrote: On Aug 17, 2011, at 3:25 PM, Harry wrote: Hi Bill I don't think this includes BLT, does it? No. That was what I was trying to say (apparently not very well, sorry!): On 17 Aug 2011, at 22:33, William Scott wrote: if CCP4 could free itself of this dependency... …then it could make use of the no-BLT version of tcl/tk provided with OS X 10.6 and 10.7. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Computer encryption matters
On 08/18/2011 04:13 AM, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Hello, Whole disk encryption is wise in case the machine is stolen. On Linux and Macs (I don't know other platforms) this is transparent and I don't see how it could trigger some runtime errors (once the computer is booted: the files are seen unencrypted by the operating system). The only concern may be that for some really I/O demanding applications (like video editing), this may slow down the video processing task. However, with decent hardware and file system, this may be just an old concern which crystallographers really don't need to care about. Another minor drawback is that you will possibly need a password to boot your machine (on Linux at least). Regards, F. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
Re: [ccp4bb] Computer encryption matters
We have no problem with encryption on Windows 7 here at NIH - Original Message - From: Harry To: CCP4BB@JISCMAIL.AC.UK Sent: Wed Aug 17 18:23:21 2011 Subject: Re: [ccp4bb] Computer encryption matters Hi John My Mac laptop has been encrypted according to MRC rules for several years and has caused no problems. Windows or Linux may behave differently, but I have no reason to think they might (until a ccp4bber tells me differently)! On 17 Aug 2011, at 20:13, Jrh wrote: > Dear Colleagues, > My institution is introducing concerted measures for improved > security via encryption of files. A laudable plan in case of loss or > theft of a computer with official files eg exams or student records > type of information stored on it. > > Files, folders or a whole disk drive can be encrypted. Whilst I can > target specific files, this could get messy and time consuming to > target them and keep track of new to-be-encrypted files. It is > tempting therefore to agree to complete encryption. However, as my > laptop is my calculations' workbench, as well as office tasks, I am > concerned that unexpected runtime errors may occur from encryption > and there may be difficulties of transferability of data files to > colleagues and students, and to eg PDB. > > Does anyone have experience of encryption? Are my anxieties > misplaced? If not, will I need to plan to separate office files, > which could then all be encrypted, from crystallographic data files/ > calculations, which could be left unencrypted. If separate treatment > is the best plan does one need two computers once more, rather than > the one laptop? A different solution would be to try to insist on an > institutional repository keeping such files. > > In anticipation, > Thankyou, > John > Prof John R Helliwell DSc Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] BLT wish
On Aug 17, 2011, at 3:25 PM, Harry wrote: > Hi Bill > > I don't think this includes BLT, does it? No. That was what I was trying to say (apparently not very well, sorry!): > > On 17 Aug 2011, at 22:33, William Scott wrote: > >> if CCP4 could free itself of this dependency... …then it could make use of the no-BLT version of tcl/tk provided with OS X 10.6 and 10.7.
Re: [ccp4bb] Computer encryption matters
Upon release of the newest MBA's from Apple there was this test on Ars http://arstechnica.com/apple/reviews/2011/08/thunder-in-the-air-ars-reviews-the-mid-2011-macbook-air.ars/3 So if you are concerned in terms of speed I would say don't worry. However never forget your password. Jürgen P.S. the above suggestion will not help you much if you are a non-Mac User On Aug 17, 2011, at 6:23 PM, Harry wrote: Hi John My Mac laptop has been encrypted according to MRC rules for several years and has caused no problems. Windows or Linux may behave differently, but I have no reason to think they might (until a ccp4bber tells me differently)! On 17 Aug 2011, at 20:13, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/ calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH .. 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://web.mac.com/bosch_lab/
Re: [ccp4bb] Computer encryption matters
Hi John My Mac laptop has been encrypted according to MRC rules for several years and has caused no problems. Windows or Linux may behave differently, but I have no reason to think they might (until a ccp4bber tells me differently)! On 17 Aug 2011, at 20:13, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/ calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] BLT wish
Yeah, it was a totally delightful interaction. So much for the Ubuntu spread
the love of humanity theme.
They have successfully migrated from figure 3 to figure 2:
http://bandcamp.tv/linux-demotivators/
As for BLT, my sense (being the unfortunate maintainer for it on fink) is that
it is dead in the water, and if CCP4 could free itself of this dependency,
those who insist upon using the GUI instead of the infinitely simpler and more
elegant command-line interface could use the OS X native port of tcl/tk.
--Bill
On Aug 17, 2011, at 6:34 AM, Edward A. Berry wrote:
> Seems to me the CCP4 change is exactly in line with the developers'
> response to wgscott's bug report at:
> https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148
>
> You have to have the BLT package, whether you shell bltwish or wish.
> Modern BLT package doesn't contain bltwish, because
> "not a bug. It doesn't make sense to provide a separate shell for each Tcl
> Extension. . . .
> just use wish for your scripts:
>
> #!/usr/bin/wish
> package require BLT
> [...] "
>
>
> Phil Evans wrote:
>> In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
>>
>> exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
>>
>> In 6.2.0 this has mutated to
>>
>> exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
>>
>> which doesn't work on our systems, see error below
>>
>> I've fixed it by changing back to the previous exec bltwish, but does this
>> new version work for other people? Should it work for me, and with what
>> version of TCL?
>>
>> (I look forward to replacing loggraph!)
>>
>> Phil
>>
>> Error in startup script: can't find package BLT
>>while executing
>> "package require BLT"
>>(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl"
>> line 47)
>>invoked from within
>> "source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
>>(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
>>
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Help with deleting reflections from an mtz file
Thanks Clemens - I knew it should be possible! Documentation didnt exactly help.. Eleanor On Wed, 17 Aug 2011 19:20:21 +0100, Clemens Vonrhein wrote: > Dear Eleanore, > > Ooops - the ccp4bb rejects attachements with *.sh ending? Let's try it > again with *.sh.txt ... > > The attached script works for me - fantastic what one can do with > SFTOOLS :-) > > Cheers > > Clemens > > On Wed, Aug 17, 2011 at 04:55:59PM +0100, Eleanor Dodson wrote: >> There are 2 rogue reflections in a data set I have here. How can I >> eliminate them? >> I thought sftools did this but i cant seem to get the syntax right. >> Short of dumping the whole file, using an editor, then >> reconstructing it I am stuck.. >> >> Eleanor
Re: [ccp4bb] Computer encryption matters
Hi, HIPAA and other regulations require systems which house patient identifiable data to have encrypted disks at our uni. Systems which house student data (e.g. SSN #'s, grades, etc) are also encrypted. Since we are doing mostly basic research or using de-identified data in structural biology, we are not required to encrypt our workstations and servers, which improves system performance, and is a big load off my shoulders! On Wed, Aug 17, 2011 at 2:13 PM, Jrh wrote: > Dear Colleagues, > My institution is introducing concerted measures for improved security via > encryption of files. A laudable plan in case of loss or theft of a computer > with official files eg exams or student records type of information stored on > it. > > Files, folders or a whole disk drive can be encrypted. Whilst I can target > specific files, this could get messy and time consuming to target them and > keep track of new to-be-encrypted files. It is tempting therefore to agree to > complete encryption. However, as my laptop is my calculations' workbench, as > well as office tasks, I am concerned that unexpected runtime errors may occur > from encryption and there may be difficulties of transferability of data > files to colleagues and students, and to eg PDB. Transferring data between encrypted and non-encrypted systems is seamless. Most of these applications encrypt your disk and optionally usb drives. Some require a password for boot or contact a centralized key server to get the keys required for decryption so that the system can boot. Our uni has a site license for Checkpoint's encryption app, but I've used truecrypt and they all allow transferring data between encrypted and non-encrypted systems without issues. HTH, Sabuj > > Does anyone have experience of encryption? Are my anxieties misplaced? If > not, will I need to plan to separate office files, which could then all be > encrypted, from crystallographic data files/calculations, which could be left > unencrypted. If separate treatment is the best plan does one need two > computers once more, rather than the one laptop? A different solution would > be to try to insist on an institutional repository keeping such files. > > In anticipation, > Thankyou, > John > Prof John R Helliwell DSc >
[ccp4bb] Computer encryption matters
Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
Re: [ccp4bb] Help with deleting reflections from an mtz file
Dear Eleanore, Ooops - the ccp4bb rejects attachements with *.sh ending? Let's try it again with *.sh.txt ... The attached script works for me - fantastic what one can do with SFTOOLS :-) Cheers Clemens On Wed, Aug 17, 2011 at 04:55:59PM +0100, Eleanor Dodson wrote: > There are 2 rogue reflections in a data set I have here. How can I > eliminate them? > I thought sftools did this but i cant seem to get the syntax right. > Short of dumping the whole file, using an editor, then > reconstructing it I am stuck.. > > Eleanor -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** #!/bin/sh # vonrh...@globalphasing.com 20110816 # input MTZ file mtz=in.mtz # output MTZ file out=out.mtz # space-separated list of h,k,l indeices to reject hkls="1,0,-25 1,0,-24" ## [ "X$mtz" = "X" ] && echo " ERROR: please define input MTZ file" && exit 1 [ "X$out" = "X" ] && echo " ERROR: please define output MTZ file" && exit 1 [ ! -f $mtz ] && echo " ERROR: input file $mtz not found" && exit 1 [ -f $out ] && echo " ERROR: output file $mtz exists (please remove and re-run)" && exit 1 for hkl in $hkls do sftools <
Re: [ccp4bb] Help with deleting reflections from an mtz file
I usually dump the whole file into text. Even wrote a little jiffy script for doing the converting back and forth: http://bl831.als.lbl.gov/~jamesh/pickup/mtz2txt Specifically, the "text version" of the MTZ file is actually an f2mtz script that will use itself as an input file to re-generate the original MTZ file (under a new name). This "script" is simply the text data with a short header containing the call to f2mtz. It can be edited in any number of creative ways, and then you just execute it to create the "new" mtz file. HTH -James Holton MAD Scientist On 8/17/2011 8:55 AM, Eleanor Dodson wrote: There are 2 rogue reflections in a data set I have here. How can I eliminate them? I thought sftools did this but i cant seem to get the syntax right. Short of dumping the whole file, using an editor, then reconstructing it I am stuck.. Eleanor
Re: [ccp4bb] COOT library
On 17 Aug 2011, at 17:10, Eric Karg wrote: > Thanks for the suggestions. I could solve the problem by using the setenv > command to the coot directory,but I still cannot use the Real Space Refine > Zone in Coot because the names are not compatible. I'm trying to build an RNA > molecule by the way. Having recently had exactly the same problem this sounds like you have the wrong dictionary in coot as well. If at start-up you don't get a line like: There are 2 data in /sw64/share/coot/lib/data/monomers/u/U.cif but instead get There are 2 data in /sw64/share/coot/lib/data/monomers/u/UR.cif Then you need to get the new dictionary from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.29.tar.gz extract it and use that to replace /path/to/coot/lib/data/monomers It seems like some of the distributed coot builds have the old dictionary (The OS X fink one definitely does because coot.info downloads http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz) and that breaks refinement for nucleic acid. Hope that helps, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] COOT library
Welcome to the quirks of RNA crystallography. It is a small community in a sea of protein crystallographers so expect to get used to work arounds to get things to work. Your answers are at the coot mailing list archives (we recently had a discussion regarding coot 0.6.2 ver 3562) . https://www.jiscmail.ac.uk/cgi-bin/webadmin?A1=ind1108&L=COOT F On Aug 17, 2011, at 10:10 AM, Eric Karg wrote: > Thanks for the suggestions. I could solve the problem by using the setenv > command to the coot directory,but I still cannot use the Real Space Refine > Zone in Coot because the names are not compatible. I'm trying to build an RNA > molecule by the way. > > Any suggestions? > > Eric - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] COOT library
Hi Eric, Once you merge the ligand coordinates to your model and do one round of refinement, the next time you open up coot and try using the real space refinement it never works (even if you import cif dictionary of your ligand) so not sure if its a problem with coot. Did anyone else had similar problems? thanks, Shya On Wed, Aug 17, 2011 at 12:10 PM, Eric Karg wrote: > Thanks for the suggestions. I could solve the problem by using the setenv > command to the coot directory,but I still cannot use the Real Space Refine > Zone in Coot because the names are not compatible. I'm trying to build an > RNA molecule by the way. > > Any suggestions? > > Eric >
Re: [ccp4bb] Help with deleting reflections from an mtz file
Am Mittwoch 17 August 2011 17:55:59 schrieb Eleanor Dodson: > There are 2 rogue reflections in a data set I have here. How can I > eliminate them? > I thought sftools did this but i cant seem to get the syntax right. > Short of dumping the whole file, using an editor, then reconstructing it > I am stuck.. > > Eleanor > Hi Eleanor, I think one could do this with DATAMAN if I remember correctly. Add least I cannot remember the right syntax. And another if one starts from the images is in xds to add the reflection to the RMOVE.HKL file. Christian
Re: [ccp4bb] COOT library
Thanks for the suggestions. I could solve the problem by using the setenv command to the coot directory,but I still cannot use the Real Space Refine Zone in Coot because the names are not compatible. I'm trying to build an RNA molecule by the way. Any suggestions? Eric
Re: [ccp4bb] Help with deleting reflections from an mtz file
Hi Eleanor, Depends on what makes them rogues. If, say, they have very large amplitudes then you could do something like: sftools read rogue.mtz select col 1 < 1 write norogue.mtz end Or if it's easier to select just the rogue reflections by some combination of "select" commands, you can do that then give the "select invert" command to get everything else. Does that help? Randy On 17 Aug 2011, at 16:55, Eleanor Dodson wrote: > There are 2 rogue reflections in a data set I have here. How can I eliminate > them? > I thought sftools did this but i cant seem to get the syntax right. Short of > dumping the whole file, using an editor, then reconstructing it I am stuck.. > > Eleanor -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] Help with deleting reflections from an mtz file
There are 2 rogue reflections in a data set I have here. How can I eliminate them? I thought sftools did this but i cant seem to get the syntax right. Short of dumping the whole file, using an editor, then reconstructing it I am stuck.. Eleanor
Re: [ccp4bb] Protein crosslinking before crystallization
Thanks all for the comments. I was thinking of crosslinking a protein that hasn't crystallized. Cystein engineering seems a good idea but depends on the availability of a good model. We'll be trying mild crosslinking using bifunctional reagents of various lengths (I suspect glutaraldehyde will not be the best option). Opher
Re: [ccp4bb] COOT library
This wrapper works for me Phil #!/bin/csh -f # # LMB wrapper script for Coot # if ($MACHTYPE == 'x86_64') then set COOT_TOP = $COOT_HOME/Coot64 else set COOT_TOP = $COOT_HOME/Coot32 endif if (! $?COOT_REFMAC_LIB_DIR) then # Dictionary location not set, use the Coot dictionaries setenv COOT_REFMAC_LIB_DIR $COOT_TOP/share/coot/lib endif echo "*** In Coot wrapper script, dictionary files set to " $COOT_REFMAC_LIB_DIR exec $COOT_TOP/bin/coot $argv On 17 Aug 2011, at 15:32, Justin Lecher wrote: > On 17/08/11 16:18, Eric Karg wrote: >> Dear all, >> >> Is there a way to make COOT use it's own libraries and not the ones from >> ccp4 which is the default? I've tried using the command export >> COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but >> it doesn't work. >> >> Thanks >> >> Eric > > Try also set CLIBD_MON to that path. > > justin > > > -- > Justin Lecher > Institute of Complex Systems > ICS-6 Structural Biochemistry > Research Centre Juelich > 52425 Juelich, Germany > phone: +49 2461 61 2117 > >
Re: [ccp4bb] COOT library
Eric, That IS the way to do it. Please make sure you have the dictionaries in the path and check your coot startup script in case it sets COOT_REFMAC_LIB_DIR back to nothing (and hence falls back to the ccp4 one). Do you get any message in your start up console? BTW which version of Coot are you using on which system!? B P.S. There is a mailing list for Coot related questions too (http://biop.ox.ac.uk/coot/mailing-list.html). Dear all, Is there a way to make COOT use it's own libraries and not the ones from ccp4 which is the default? I've tried using the command export COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but it doesn't work. Thanks Eric - No virus found in this message. Checked by AVG - www.avg.com Version: 10.0.1392 / Virus Database: 1520/3839 - Release Date: 08/16/11
Re: [ccp4bb] COOT library
On 17/08/11 16:18, Eric Karg wrote: > Dear all, > > Is there a way to make COOT use it's own libraries and not the ones from ccp4 > which is the default? I've tried using the command export > COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but > it doesn't work. > > Thanks > > Eric Try also set CLIBD_MON to that path. justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] COOT library
Dear all, Is there a way to make COOT use it's own libraries and not the ones from ccp4 which is the default? I've tried using the command export COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but it doesn't work. Thanks Eric
Re: [ccp4bb] BLT wish
Seems to me the CCP4 change is exactly in line with the developers'
response to wgscott's bug report at:
https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148
You have to have the BLT package, whether you shell bltwish or wish.
Modern BLT package doesn't contain bltwish, because
"not a bug. It doesn't make sense to provide a separate shell for each Tcl
Extension. . . .
just use wish for your scripts:
#!/usr/bin/wish
package require BLT
[...] "
Phil Evans wrote:
In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
In 6.2.0 this has mutated to
exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
which doesn't work on our systems, see error below
I've fixed it by changing back to the previous exec bltwish, but does this new
version work for other people? Should it work for me, and with what version of
TCL?
(I look forward to replacing loggraph!)
Phil
Error in startup script: can't find package BLT
while executing
"package require BLT"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl" line
47)
invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
Re: [ccp4bb] conversion of ccdc cif to pdb
Dear Christian, Sometime ago, I ran into the same problems as you describe. I think I used an iUCR program to do the conversion. However, extensive manual editing was still necessary. The problem was that the cif file had long atoms names (5 characters), which got truncated upon conversion, resulting in different atoms having the same name. This probably explains the behavior you observe with coot. I am not aware of a program which automatically invents new, unique atom names after truncation, so I am afraid you will have to do it using your favorite editor. You should also check the position of the atom name, so e.g. a C-alpha (CA) atom does not get interpreted as a calcium. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Christian Roth Sent: Wednesday, August 17, 2011 10:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] conversion of ccdc cif to pdb Dear all, I want convert a small molecule cif into pdb. Unfortunately coordvonv failed with the following error message: CCP4I TERMINATION STATUS 0 "At line 537 of file /usr/local/xtal/ccp4-6.1.3/src/coordconv.f Fortran runtime error: Bad value during floating point read I am able to read the file with pymol and see the structure, unfortunatley one cannot isolate chains or atoms. Some atoms exists twice and if one delete it in Coot one delete always more than one atom and that is not what I want. Does anyone know a good programm to deal with cif file or to convert it properly in a format? Thanks in advance Christian
Re: [ccp4bb] BLT wish
Dear Phil,
for me (RHEL 6.1, 64-bit, ccp4 6.2), loggraph works with wish but
requires bltwish. The command is
exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
but if I set
export CCP4I_TCLTK=/sharedSoftware/ActiveTcl-8.5/bin
I get the same error that you report because ActiveTcl-8.5 doesn't
contain bltwish, which is required in loggraph.tcl. When I set
export CCP4I_TCLTK=$CCP4_MASTER/tcltk++/bin
I don't get the error.
Andreas
On 17/08/2011 10:22, Phil Evans wrote:
In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
In 6.2.0 this has mutated to
exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
which doesn't work on our systems, see error below
I've fixed it by changing back to the previous exec bltwish, but does this new
version work for other people? Should it work for me, and with what version of
TCL?
(I look forward to replacing loggraph!)
Phil
Error in startup script: can't find package BLT
while executing
"package require BLT"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl" line
47)
invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] BLT wish
On 17/08/11 10:49, Phil Evans wrote: Roll on the loggraph replacement! Next month ?
Re: [ccp4bb] BLT wish
It doesn't seem to work out of the box on Centos5.6, nor on Scientific Linux 6.
On SL6 I think we had to install yet another TCLTK from somewhere (can't
remember) to get BLT, and with that one using "wish" does work
Roll on the loggraph replacement!
Phil
On 17 Aug 2011, at 10:38, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi Phil,
>
> 'wish' works on Debian (stable upwards) (and therefore probably also on
> Ubuntu) where blt is hidden in a library, and it works greatly - I used
> to do the opposite, i.e. changing bltwish into wish but e.g. loggraph
> did not work properly that way.
>
> Best wishes, Tim
>
> On 08/17/2011 11:22 AM, Phil Evans wrote:
>> In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
>>
>> exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
>>
>> In 6.2.0 this has mutated to
>>
>> exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
>>
>> which doesn't work on our systems, see error below
>>
>> I've fixed it by changing back to the previous exec bltwish, but does this
>> new version work for other people? Should it work for me, and with what
>> version of TCL?
>>
>> (I look forward to replacing loggraph!)
>>
>> Phil
>>
>> Error in startup script: can't find package BLT
>> while executing
>> "package require BLT"
>> (file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl"
>> line 47)
>> invoked from within
>> "source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
>> (file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.10 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFOS4wOUxlJ7aRr7hoRAk2HAKDxGHgG7CPreyN2jgNs3vIVlHJ57ACeLATc
> I5xWGzXb1I38VEPgDS2qUms=
> =5UU/
> -END PGP SIGNATURE-
Re: [ccp4bb] BLT wish
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Phil,
'wish' works on Debian (stable upwards) (and therefore probably also on
Ubuntu) where blt is hidden in a library, and it works greatly - I used
to do the opposite, i.e. changing bltwish into wish but e.g. loggraph
did not work properly that way.
Best wishes, Tim
On 08/17/2011 11:22 AM, Phil Evans wrote:
> In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
>
> exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
>
> In 6.2.0 this has mutated to
>
> exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
>
> which doesn't work on our systems, see error below
>
> I've fixed it by changing back to the previous exec bltwish, but does this
> new version work for other people? Should it work for me, and with what
> version of TCL?
>
> (I look forward to replacing loggraph!)
>
> Phil
>
> Error in startup script: can't find package BLT
>while executing
> "package require BLT"
>(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl"
> line 47)
>invoked from within
> "source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
>(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFOS4wOUxlJ7aRr7hoRAk2HAKDxGHgG7CPreyN2jgNs3vIVlHJ57ACeLATc
I5xWGzXb1I38VEPgDS2qUms=
=5UU/
-END PGP SIGNATURE-
Re: [ccp4bb] conversion of ccdc cif to pdb
Hi Christian, we use openbabel for this kind of thing, I'm sure you'll find the file formats you want to interconvert among the long list it supports: http://openbabel.org/wiki/Category:Formats Cheers -- Ian On Wed, Aug 17, 2011 at 9:20 AM, Christian Roth < christian.r...@bbz.uni-leipzig.de> wrote: > Dear all, > > I want convert a small molecule cif into pdb. Unfortunately coordvonv > failed > with the following error message: > CCP4I TERMINATION STATUS 0 "At line 537 of file > /usr/local/xtal/ccp4-6.1.3/src/coordconv.f Fortran runtime error: Bad value > during floating point read > > I am able to read the file with pymol and see the structure, unfortunatley > one > cannot isolate chains or atoms. Some atoms exists twice and if one delete > it > in Coot one delete always more than one atom and that is not what I want. > Does anyone know a good programm to deal with cif file or to convert it > properly in a format? > > Thanks in advance > > Christian >
[ccp4bb] BLT wish
In previous CCP4 releases CCP4/ccp4i/bin/loggraph used "bltwish"
exec $CCP4I_TCLTK/bltwish "$0" -- ${1+"$@"}
In 6.2.0 this has mutated to
exec $CCP4I_TCLTK/wish "$0" -- ${1+"$@"}
which doesn't work on our systems, see error below
I've fixed it by changing back to the previous exec bltwish, but does this new
version work for other people? Should it work for me, and with what version of
TCL?
(I look forward to replacing loggraph!)
Phil
Error in startup script: can't find package BLT
while executing
"package require BLT"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl" line
47)
invoked from within
"source [file join $env(CCP4I_TOP) bin loggraph.tcl]"
(file "/public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph" line 5)
[ccp4bb] conversion of ccdc cif to pdb
Dear all, I want convert a small molecule cif into pdb. Unfortunately coordvonv failed with the following error message: CCP4I TERMINATION STATUS 0 "At line 537 of file /usr/local/xtal/ccp4-6.1.3/src/coordconv.f Fortran runtime error: Bad value during floating point read I am able to read the file with pymol and see the structure, unfortunatley one cannot isolate chains or atoms. Some atoms exists twice and if one delete it in Coot one delete always more than one atom and that is not what I want. Does anyone know a good programm to deal with cif file or to convert it properly in a format? Thanks in advance Christian
