Re: [ccp4bb] in vitro Tyr phosphorylation
The kinase domain of FAK can be made constitutively active by a mutation and expressed in E. coli. It's called Super FAK Kinase. But i am afraid it is rather specific. If you don't get a better lead I can send you the sequence and a reference. Gloria Borgstahl wrote: Does anyone know of a good way to phosphorylate the Tyr on a protein for structural studies? Is there a generic kinase that can be coexpressed or purified for phosphorylation? The pCMF Amber codon system is very expensive and Glu really doesn't mimic pTyr all that well. Any ideas/help would be appreciated, G
Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Junyu, You can test cryo conditions conveniently in the absence of your crystals if you have access to e.g. an inhouse machine. Prepare your solutions with the usual suspects (PEG400; PEG400+glycerol; butanediol; Na Malonate etc. pp.) at various concentrations, pick up a large as possible drop with a nylon loop and take a shot to see if you have ice rings. Try to be on the safe side with respect to the decision about the minimal concentration because the presence of the crystal might give a slightly different result. Best, Tim On 12/16/2013 10:36 PM, Xiao, Junyu wrote: Dear all, sorry if this topic does not interest you. I wonder whether anyone has experience with freezing crystals grown in ~0.2 M Magnesium Formate. Garman and Mitchell suggested that A major anomaly is solution 44, 0.2 M magnesium formate, which requires 50% glycerol for cryoprotection in their 1996 paper (J Appl. Cryst. 29, 584-587). Since 50% glycerol is kind of harsh, I wonder whether anyone has tried alternative cryo protectant. Your kind help will be highly appreciated. Best regards, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsBJ/UxlJ7aRr7hoRApCiAJ0b3LyawgscAsIzwFUUHNDqRSplPwCeOZPv pF9iloWrCgMjIwo4hKlAgN8= =l4tU -END PGP SIGNATURE-
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsBQ+UxlJ7aRr7hoRAk2wAJ9MauWFkWoiW34xYGJVVPpFTD1NTQCgiNdY +h052qPU7DNQoRlZOGg75Os= =oema -END PGP SIGNATURE-
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
Thanks so much. XDS program is a very good example for multi-core cpu processing. I love it. I also have a macbook. Though a notebook, it often runs CCP4 program more quickly than on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsBQ+UxlJ7aRr7hoRAk2wAJ9MauWFkWoiW34xYGJVVPpFTD1NTQCgiNdY +h052qPU7DNQoRlZOGg75Os= =oema -END PGP SIGNATURE-
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, Without being aware of the various means to parallelise a computer program I would be surprised if refmac5 was parallelised for MacOSX but not for Linux, although I am sure Garib would correct me if I was wrong. Maybe you only have the impression that refmac5 uses several cores on MacOSX? Regards, Tim On 12/17/2013 01:05 PM, Chang Qing wrote: Thanks so much. XDS program is a very good example for multi-core cpu processing. I love it. I also have a macbook. Though a notebook, it often runs CCP4 program more quickly than on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsEI+UxlJ7aRr7hoRAiIiAKDCWKpTFw1nin+BCAdXW7cLMjKq7QCg7EU3 MiuWuXad/KGgBLd6Q8aN0W0= =RiQ5 -END PGP SIGNATURE-
Re: [ccp4bb] Heavy atom sites
Yes - mlphare did, but so does Phaser_ep E On 16 December 2013 18:46, Bosch, Juergen jubo...@jhsph.edu wrote: Didn't mlphare use to print those values in the log file ? Jürgen On Dec 15, 2013, at 4:29 PM, David Schuller dj...@cornell.edu wrote: I have some SIRAS data of a known structure. I want to get the isomorphous and anomalous occupancy and phasing power from my data. What's the best software to do this? -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
Dear Tim Yes, it is just my impression. I don't know how to test it. As now most of computers have multi-core CPU, I really hope CCP4 programs can be paralleled. Thank you so much for answering my questions. All my best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, Without being aware of the various means to parallelise a computer program I would be surprised if refmac5 was parallelised for MacOSX but not for Linux, although I am sure Garib would correct me if I was wrong. Maybe you only have the impression that refmac5 uses several cores on MacOSX? Regards, Tim On 12/17/2013 01:05 PM, Chang Qing wrote: Thanks so much. XDS program is a very good example for multi-core cpu processing. I love it. I also have a macbook. Though a notebook, it often runs CCP4 program more quickly than on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsEI+UxlJ7aRr7hoRAiIiAKDCWKpTFw1nin+BCAdXW7cLMjKq7QCg7EU3 MiuWuXad/KGgBLd6Q8aN0W0= =RiQ5 -END PGP SIGNATURE-
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Chang,
some time back people would benefit from the computational time (or
e.g. data collection time) to get a coffee, lean back and think about
what was going on - this was often very efficient and not rarely more
effective than the false perception of computers being able to think
for oneself ;-)
You can also parallelise programs yourself by means of shell scripting
for example if you want to test several parameter settings. The
following e.g. is a script to keep an 8-core computer busy for a
couple of days even if shelxl were not parallelised:
#!/bin/bash
for i in $(seq -w 99); do
test -f kcross_set${i}1.lst || nohup shelxl kcross_set${i}1 -t1
/dev/null pid1=$!
test -f kcross_set${i}2.lst || nohup shelxl kcross_set${i}2 -t1
/dev/null pid2=$!
test -f kcross_set${i}3.lst || nohup shelxl kcross_set${i}3 -t1
/dev/null pid3=$!
test -f kcross_set${i}4.lst || nohup shelxl kcross_set${i}4 -t1
/dev/null pid4=$!
test -f kcross_set${i}5.lst || nohup shelxl kcross_set${i}5 -t1
/dev/null pid5=$!
test -f kcross_set${i}6.lst || nohup shelxl kcross_set${i}6 -t1
/dev/null pid6=$!
test -f kcross_set${i}6.lst || nohup shelxl kcross_set${i}7 -t1
/dev/null pid7=$!
wait $pid1
wait $pid2
wait $pid3
wait $pid4
wait $pid5
wait $pid6
wait $pid7
done
Be careful with such scripts, though, because you may easily stall the
computer busy with swapping ;-)
Best,
Tim
On 12/17/2013 01:56 PM, Chang Qing wrote:
Dear Tim
Yes, it is just my impression. I don't know how to test it. As now
most of computers have multi-core CPU, I really hope CCP4 programs
can be paralleled. Thank you so much for answering my questions.
All my best
Chang
2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de
Dear Chang,
Without being aware of the various means to parallelise a computer
program I would be surprised if refmac5 was parallelised for
MacOSX but not for Linux, although I am sure Garib would correct me
if I was wrong. Maybe you only have the impression that refmac5
uses several cores on MacOSX?
Regards, Tim
On 12/17/2013 01:05 PM, Chang Qing wrote:
Thanks so much. XDS program is a very good example for
multi-core cpu processing. I love it. I also have a macbook.
Though a notebook, it often runs CCP4 program more quickly
than on desktop computer. The programs, for example refmac5,
seem to use multi-core on OSX and single core on linux. Is
that mean CCP4 runs more efficiently on OSX than linux?
Best
Chang
2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de
Dear Chang,
this is hardly a matter of configuration but a question of
programming (meaning you cannot change it unless you modify
the source code and recompile). You can run a program of
which you know it is parallelised, e.g. XDS, shelxl, shelxd,
and check with the command 'top' that your %CPU is about
400%.
You can also get the program i7z for more detailed
information about the status of your CPUs.
Phaser is parallelised, but I dare say it is rather an
exception within the ccp4 suite.
So all you can do is encourage the developers of
cpu-demanding programs to spend time on parallelising their
code - XDS is one of the most impressive examples of how much
this can be worth in the context of acceptance and
propagation.
Best, Tim
On 12/17/2013 02:51 AM, Chang Qing wrote:
Dear all
I just installed CCP4 6.4 on Ubuntu 12.1. The program
can work. I found it just used 1 processor instead of
4( Intel i5) for data solving. Does anyone know how to
config CPU so that all processors can be used.
Thanks
Chang
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/
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wJNAj9z2auQaQAjjmKs0B6o=
=KWlq
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Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
Dear Chang, Some CCP4 progs can be used with a multi-core machine, using OpenMP threads (including refmac it would appear). You will need to compile the code from source rather than taking the binary versions, which is much less convenient. Even if the CCP4 apps are not parallel themselves, they can access a parallel version of libraries e.g. FFTW, LAPACK. Again you will probably need to compile CCP4 from source and link with the correct libraries. The third option (as Tim described) is task-farming. Bioinformations typically use our HPC in this way. Given that you do not want to overtax your machine you might set OMP_THREAD_NUM=2 which would give you less than 2x speedup, I am not sure it is worth the hassle. Adam
Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate
I find that odd because the first structure I ever worked on was a DNA oligonucleotide grown in 0.2 M magnesium formate and it did not require cryoprotection at all when flash cooled directly in the cryostream. I learned from Ned Seeman's group a long while back that Mg2+ itself worked reasonably well as a cryoprotectant at high concentrations. We routinely freeze DNA crystals with 120 mM Mg formate and 10% MPD. --paul On 12/16/2013 04:36 PM, Xiao, Junyu wrote: Dear all, sorry if this topic does not interest you. I wonder whether anyone has experience with freezing crystals grown in ~0.2 M Magnesium Formate. Garman and Mitchell suggested that A major anomaly is solution 44, 0.2 M magnesium formate, which requires 50% glycerol for cryoprotection in their 1996 paper (J Appl. Cryst. 29, 584-587). Since 50% glycerol is kind of harsh, I wonder whether anyone has tried alternative cryo protectant. Your kind help will be highly appreciated. Best regards, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684
Re: [ccp4bb] Cryo solution for crystals grown in magnesium formate
You can increase the formate concentration and it will be a cryoprotectant on its own. Test increasing amounts until you find the concentrationthat freezed clear as glass and the transfer your crystal to this. We did this with sodium formate at 7 M quite easily. On Tue, Dec 17, 2013 at 2:59 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Junyu, You can test cryo conditions conveniently in the absence of your crystals if you have access to e.g. an inhouse machine. Prepare your solutions with the usual suspects (PEG400; PEG400+glycerol; butanediol; Na Malonate etc. pp.) at various concentrations, pick up a large as possible drop with a nylon loop and take a shot to see if you have ice rings. Try to be on the safe side with respect to the decision about the minimal concentration because the presence of the crystal might give a slightly different result. Best, Tim On 12/16/2013 10:36 PM, Xiao, Junyu wrote: Dear all, sorry if this topic does not interest you. I wonder whether anyone has experience with freezing crystals grown in ~0.2 M Magnesium Formate. Garman and Mitchell suggested that A major anomaly is solution 44, 0.2 M magnesium formate, which requires 50% glycerol for cryoprotection in their 1996 paper (J Appl. Cryst. 29, 584-587). Since 50% glycerol is kind of harsh, I wonder whether anyone has tried alternative cryo protectant. Your kind help will be highly appreciated. Best regards, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsBJ/UxlJ7aRr7hoRApCiAJ0b3LyawgscAsIzwFUUHNDqRSplPwCeOZPv pF9iloWrCgMjIwo4hKlAgN8= =l4tU -END PGP SIGNATURE-
Re: [ccp4bb] in vitro Tyr phosphorylation
Thank you all for your suggestions, I copied them below I also found a paper for making Src and Abl catalytic domains Protein Science Dec 2005 --- Before, I found a paper of Bhandari R (2000) where they describe the co-expression of tyrosine kinase EphB1 (attached file). I haven’t checked how generic the kinase is. Kind regards Seppe Leysen --- Guillermo Montoya gmont...@cnio.es I do not have the full reference here But there is a febs lett paper from crhistoph muller group where they co express stat transcription factor with a kinase to obtain the dimer Dimerisation depends on tyr phosphorylation Hope it helps G. - Hi, This is in response to your post on the CCP4 bulletin board. We either express Src independently and mix it with the target protein to be phosphorylated in the presence of ATP at 37°C (works well) or co-express the target protein with a non-specific PTK. Best Nicolas Nassar, PhD On Tue, Dec 17, 2013 at 2:13 AM, Edward A. Berry ber...@upstate.edu wrote: The kinase domain of FAK can be made constitutively active by a mutation and expressed in E. coli. It's called Super FAK Kinase. But i am afraid it is rather specific. If you don't get a better lead I can send you the sequence and a reference. Gloria Borgstahl wrote: Does anyone know of a good way to phosphorylate the Tyr on a protein for structural studies? Is there a generic kinase that can be coexpressed or purified for phosphorylation? The pCMF Amber codon system is very expensive and Glu really doesn't mimic pTyr all that well. Any ideas/help would be appreciated, G
Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz
Dear Partha and Uli, We haven't tested it on SLES11 and we overlooked this problem. It will be fixed in updates. For now as a workaround do: ln -s libgfortran.so.3.0.0 $CCP4/lib/libgfortran.so.3 (hopefully works, I cannot test it now) Usually the quickest way to have such problems solved is to email CCP4 helpdesk (c...@ccp4.ac.uk). Marcin On Mon, Dec 16, 2013 at 12:53:58PM -0500, Parthasarathy Sampathkumar wrote: Yes Uli. I have the same issue, but not solve it yet :-( Partha On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.de wrote: Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the file box for the data file: CCP4i encountered an error when trying to extract the data from data.mtz. You can view the output from the mtzdump program etc. + crash of the GUI. Now, running mtzdump gives me this: http://www.hkl-xray.com/data-upload-form-and-bug-report./mtzdump: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.1' not found (required by /xprogs/CCP4/CCP4-6.4.0/destination/ccp4-6.4.0/bin/../lib/libccp4f.so.0) In /usr/lib64 I have softlinked libgfortran.so.3 - libgfortran.so.3.0.0 (did so in 2011). I am not sure what I need to update here and how. I am running Novell's SLES 11 on a 64 bit system with the libgfortran43 runtime library installed. I have also checked file permissions (incl. tmp directories), and I cannot find anything obvious. I cannot remember having had similar problems with v6.3.0 in the beginning. Has anyone encountered the same problem and solved it yet? My apologies if this has been discussed already; I searched the archive and I couldn't find a similar thread. Cheers, Uli --- dr ulrich gohlke *staff scientist - m**acromolecular structure and interaction* max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ -- Scanned by iCritical.
