Re: [ccp4bb] scala maxbat compile problems
jpd, I have seen this type of error message in situations where some memory limit was exceeded. Based on googling with 'common relocation truncated to fit ', the memory limit has something to do with a COMMON block exceeding its max size, see - http://coding.derkeiler.com/Archive/Fortran/comp.lang.fortran/2008-10/msg00471.html Other than that posting suggests, it is the ifort compiler which understands -mcmodel=medium ; how the same is done with gfortran I don't know. Furthermore, more googling reveals that -mcmodel=medium also seems to require -i-dynamic (as an option to ifort). So I think you should try ifort compilation whith those options - but it might mean that also some of the libraries have to be recompiled. HTH, Kay jp d schrieb: hi more information. scala compiles with maxbat set anywto 11750, but fails with maxbat 11760 jpd --- On Fri, 10/9/09, jp d yo...@yahoo.com wrote: From: jp d yo...@yahoo.com Subject: [ccp4bb] scala maxbat compile problems To: CCP4BB@JISCMAIL.AC.UK Date: Friday, October 9, 2009, 3:16 PM hi, we were hitting maxbat limits so i downloaded the source and increased maxbat whereever i found it to 2 compiling fails at scala with errors like this: scala.f:(.text+0x5e0): relocation truncated to fit: R_X86_64_32S against symbol `rfile_' defined in COMMON section in scala.o scala.f:(.text+0x601): relocation truncated to fit: R_X86_64_32S against symbol `rfile_' defined in COMMON section in scala.o Ubuntu 8 , 64 bit , ccp4-6.1.2 is there some configure option i am missing? thanks jpd -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] pdbcur failed with the error message 'child process exited abnormally'
The big problem here is that it doesn't recognise the NOANISOU keyword. So I presume that you are picking up an old version of CCP4, or more likely a Coot version of pdbcur. Mmmm the fact that the banner doesn't report user or date or time suggests a dodgy version. I would have to defer to a Mac person on how to set this up properly. I guess you should do a which pdbcur in a terminal window to confirm the problem, and then fix your PATH somehow. As Fred says, it is much easier to use grep -v ANISOU foo.pdb and I believe you can do this even on a Mac :) Martyn -Original Message- From: CCP4 bulletin board on behalf of Raja Dey Sent: Sat 10/10/2009 12:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] pdbcur failed with the error message 'child process exited abnormally' Hello, I remember PDBCUR was running before updating CCP4 to 6.1.1 in my macbook. I am trying to remove the aniso U's from a pdb file and I stuck. I might need some additional setup for this to run. Is there anyone who can tell what to do? I attached the error message below: ### ### ### ### CCP PROGRAM SUITE: pdbcur ## ### User: Run date: Run time: Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. PDB file /Users/rajadey/yong/cns/alternate/final/phenix/may21_1_1_001.pdb has been read in. -- Input cards Data line--- NOANISOU Unrecognised keyword NOANISOU *** * Information from CCP4Interface script *** The program run with command: pdbcur XYZIN /Users/rajadey/yong/cns/alternate/final/phenix/may21_1_1_001.pdb XYZOUT /Users/rajadey/yong/cns/alternate/final/phenix/may21_pdbset1.pdb has failed with error message child process exited abnormally Thanks... Raja Try the new Yahoo! India Homepage. Click here. http://in.yahoo.com/trynew -- Scanned by iCritical.
[ccp4bb] To get the crystal faster...
Dear crystallographers, Sorry for the non-ccp4 query. I am new to this field and need some suggestions. My question is, why some protein takes longer time to crystallize, say 6-8 months, and it is the only condition to get the crystals.? What are the ways to get the crystals faster. The crystal appears with 60% of 2-Methyl, 2-4 Pentane Diol and only at 4 degree with very low concentration of NaCl. I have got some of the sugggestions earlier from the CCP4-discussion board for microseeding, but it did not work. All suggestions from the experts are welcome. Thanks. James
Re: [ccp4bb] To get the crystal faster...
It will help more if we send it to James ;) On Oct 11, 2009, at 9:15 AM, gauri misra wrote: Dear James, As there are indications of protein degradation that have been suggested in previous postings, i think adding some protease inhibitors right at the stage of purification may provide some help. Moreover, you can also try various additives as specified in one of the Hampton screens (certainly if the protein requires some cofactor for its functioning that would be the priority as an additive). You have just given one condition. Is it that crystals are visible only in this particular condition? If there are positive results in some other condition we can think of playing around that too as an alternative strategy. Hope this little piece of suggestion may help you at some point. Best wishes Gauri
Re: [ccp4bb] To get the crystal faster...
Hi James, have you tried limited proteolysis on your protein and see if you can identify a stable fragment. Then re-clone and re-crystallize your protein. Or a very stupid suggestion, how does your size exclusion peak look like ? What you're not running your protein over a SEC to polish it ? Good luck, Jürgen On Oct 11, 2009, at 11:27 AM, james09 pruza wrote: Dear crystallographers, Sorry for the non-ccp4 query. I am new to this field and need some suggestions. My question is, why some protein takes longer time to crystallize, say 6-8 months, and it is the only condition to get the crystals.? What are the ways to get the crystals faster. The crystal appears with 60% of 2-Methyl, 2-4 Pentane Diol and only at 4 degree with very low concentration of NaCl. I have got some of the sugggestions earlier from the CCP4-discussion board for microseeding, but it did not work. All suggestions from the experts are welcome. Thanks. James - 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/
[ccp4bb] To set a crystal tray with protein and Trypsin protease.
Hello, I am sorry to put this question which didn¹t related to the CCP4 software. I couldn¹t get the crystals from the protein only. So I want to try the different way to work it out. I hear that it is possible to set a crystal tray of protein with Trypsin protease. I will be very appreciated about who will provide some detail of this method about how to do this., e.g. How much trypsin shall I add into the protein, How long shall I mix protease with the proteins before I set the tray. Thanks for all. I will also put on the summary of all the answers. Another question is about protein express in insect cell. 10% of my protein was degradated after 1st purification. Is anyway that I can prohibit this degradation? Thanks Jing
[ccp4bb] problems with molprobity in coot
Hi everyone, I am trying to use molprobity to check a structure in coot (platform is 64-bit vista). I followed the instructions found here to set up molprobity: http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html . From the logs, it seems like reduce runs OK (it says that it Added 6076 hydrogens). However, at the very end, I get the message BL WARNING:: reduce didnt run ok, so stop here! It seems like probe never runs. Does anyone know how to solve this? Thanks, Thomas Cleveland (graduate student, Johns Hopkins University)
Re: [ccp4bb] To get the crystal faster...
Sometimes it is better that it takes time for crystals to appear. Remember that crystallisation is a purification procedure. A way to decrease the speed of crystallisation is to use Dunlop's and Haze's drop dilution method (K. V. Dunlop B. Hazes (2003). When less is more: a more efficient vapour-diffusion protocol. Acta Cryst. D59, 1797-1800). HTH, Fred. attachment: Frederic_Vellieux.vcf
Re: [ccp4bb] To set a crystal tray with protein and Trypsin protease.
Hi Jing, Methods to perform In site proteolysis are available in the following publications: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005094 http://www.nature.com/nmeth/journal/v4/n12/abs/nmeth1118.html Good Luck, -Partha On Sun, Oct 11, 2009 at 5:13 PM, jwangliang jwangli...@gmail.com wrote: Hello, I am sorry to put this question which didn’t related to the CCP4 software. I couldn’t get the crystals from the protein only. So I want to try the different way to work it out. I hear that it is possible to set a crystal tray of protein with Trypsin protease. I will be very appreciated about who will provide some detail of this method about how to do this., e.g. How much trypsin shall I add into the protein, How long shall I mix protease with the proteins before I set the tray. Thanks for all. I will also put on the summary of all the answers. Another question is about protein express in insect cell. 10% of my protein was degradated after 1st purification. Is anyway that I can prohibit this degradation? Thanks Jing
Re: [ccp4bb] To set a crystal tray with protein and Trypsin protease.
It should be In situ and not 'In site'. Sorry for the typo error. -Partha On Sun, Oct 11, 2009 at 9:59 PM, Parthasarathy Sampathkumar spart...@gmail.com wrote: Hi Jing, Methods to perform In site proteolysis are available in the following publications: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005094 http://www.nature.com/nmeth/journal/v4/n12/abs/nmeth1118.html Good Luck, -Partha On Sun, Oct 11, 2009 at 5:13 PM, jwangliang jwangli...@gmail.com wrote: Hello, I am sorry to put this question which didn’t related to the CCP4 software. I couldn’t get the crystals from the protein only. So I want to try the different way to work it out. I hear that it is possible to set a crystal tray of protein with Trypsin protease. I will be very appreciated about who will provide some detail of this method about how to do this., e.g. How much trypsin shall I add into the protein, How long shall I mix protease with the proteins before I set the tray. Thanks for all. I will also put on the summary of all the answers. Another question is about protein express in insect cell. 10% of my protein was degradated after 1st purification. Is anyway that I can prohibit this degradation? Thanks Jing
