Re: [ccp4bb] CNS 1.2.2 binary running out of memory

Hi everyone and thanks for your help with my cns problems. I am sure that some settings in my file were leading to an escalation in the memory requirement. Since a significant portion of my model was polyala , I had edited my anneal.inp file and increased the torsion_maxlength , torsion_maxtree and

Re: [ccp4bb] Bacterial induction at 18C

Raji aside from the possibilites of toxic protein as already mentioned.. we had great results with overnight induction at 20oC for a protein that was somewhat insoluble at 37oC. One thing that might work for you is to grow the cells to OD 0.5 then lower the temperature to say 18 or 20. After

Re: [ccp4bb] CNS 1.2.2 binary running out of memory

CCP4 bulletin board wrote on 04/30/2008 03:33:32 PM: > Hi > Since I am not on the cnsbb yet I am posting this here. > I downloaded the cns 1.2.2 intel build and was trying to run a > simulated annealing refinement on my macbook pro ( Intel) running 10.5.2 . > (snip) > > The detailed error is po

Re: [ccp4bb] CNS 1.2.2 binary running out of memory

You need to use the syntax: unlimit stacksize unlimit datasize unlimit memoryuse and I have these in my .cshrc I can get this under OSX 10.5 (albeit on an old G5 chip machine): cputime unlimited filesize unlimited datasize unlimited stacksize65532 kbytes coredumpsize unlimite

[ccp4bb] CNS 1.2.2 binary running out of memory

Hi Since I am not on the cnsbb yet I am posting this here. I downloaded the cns 1.2.2 intel build and was trying to run a simulated annealing refinement on my macbook pro ( Intel) running 10.5.2 . However the annealing job crashes roughly 40 minutes into the refinement with the following message

[ccp4bb] Need Solve/Resolve advice

CCP4bb subcribers, I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve outputs three sites: pdb coordinates fractional coordinates -15.833 35.392 38.440 0.0486 0.4315 0.1615 7.834 76.449 38.475 0.5487 0.9320 0.1617 16.310 60.866 37.449 0.5432

Re: [ccp4bb] Bacterial induction at 18C

Thanks to everyone for all your suggestions. I am growing the cultures as we speak and have increased the temp to 22C and plan to harvest in about 6-8 hrs. Thanks for the Q7 rule. I read it before but I couldn't remember exactly and a quick-and-dirty Google and Pubmed search did not bring it up

[ccp4bb] Synchrotron beam time at EMBL Hamburg

This is a gentle reminder of our call for beam time applications at EMBL Hamburg that we circulated a few weeks ago. We kindly ask you to complete your beam time proposal by the deadline of ---> 16 May 2008 < If you have already taken action, please ignore this message. --

Re: [ccp4bb] Bacterial induction at 18C

Hi Raji, Any possibility that your protein lyzed the E. coli. Some proteins do that. It's unlikely the antibiotics are the problem. You have to find out when the bugs start to lyze and harvest before that time point. In addition, lower the induction temperature further down in case the lysis is du

Re: [ccp4bb] Low resolution structure refinement

I suspect if you compare Ramachandran plots you'll find that despite the slightly higher Rfree, the ncs-restrained coordinates already have better geometry. You probably need to optimize your ncs restraints. For example: - remove the restraints all side chains that are in different crystal pa

Re: [ccp4bb] Bacterial induction at 18C

Dear Raji, I have expressed proteins in E. coli at 18ºC (and below that) with Amp+Kan+Chl and I've never had any problem with cell lysis. I usually grow cells at 37ºC and then cool the cultures down to the desired temperature before induction. I don't recomend growing your cultures at low temperat

Re: [ccp4bb] Bacterial induction at 18C

Raji, I am working with E. coli cells co-transformed with two plasmids and I find that my cells lyse following overnight inductions at 18C. Sounds more like a phage contamination. The phage becomes active as soon as the cells "energy level" decreases, e.g upon induction. We had once the sam

Re: [ccp4bb] Bacterial induction at 18C

Are you sure it is not a phage infection that is causing lysis of your cells? Christopher J. Law, PhD Skirball Institute of Biomolecular Medicine, Structural Biology (3-5), New York University Medical Center, 540 First Avenue, New York, NY 10016, USA. 2008/4/30 Raji Edayathumangalam <[EMAIL PROTE

[ccp4bb] Bacterial induction at 18C

Hi Folks, I am working with E. coli cells co-transformed with two plasmids and I find that my cells lyse following overnight inductions at 18C. I suspect (among many things) that Ampicillin+ Chloramphenicol+ Kanamycin in the medium may be the source of my woes. My colleagues have suggested grow

Re: [ccp4bb] xds installation

Eike Schulz schrieb: Hello everyone, I still consider myself new to Linux so this is probably just a minor problem but currently I can't find a way around it - I hope that somebody can help me. Using the xds_inst script to install XDS I get the following error messages: $PATH/html_doc/xds_inst

Re: [ccp4bb] Are Calcium Citrate Crystals A Common False Positive?

Calcium citrate does have a relatively low solubility (~15 mM in the cold), and its solubility decreases as the temperature goes up. Thus, getting calcium citrate crystals is a possibility if both are at 200 mM. However, you can get sodium citrate up to ~1.4 M at least, depending on the p

[ccp4bb] Rigaku X-ray Generator RUH3 for Sale

Dear Colleagues, we have an Rigaku RINT2000 Series, horizontal type rotaflex (RU-H3) rotating anode X-ray generator for sale at a nominal price plus lots of spare parts. The offer does not include the optics, the goniometer, any detector nor a water-cooling system. Included are all other units su

Re: [ccp4bb] xds installation

Dear Eike, Installing XDS is in fact pretty straightforward - if you unpack the XDS tarball containing the executables "somewhere sensible" - e.g. /opt/px/xds or /usr/local/xds then put wherever you unpacked this in your path it will work fine. You can do this by adding this to your .bashrc file:

[ccp4bb] xds installation

Hello everyone, I still consider myself new to Linux so this is probably just a minor problem but currently I can't find a way around it - I hope that somebody can help me. Using the xds_inst script to install XDS I get the following error messages: $PATH/html_doc/xds_inst: line 20: setenv: comm

Re: [ccp4bb] discontinuous data wedges in XDS

Hi Bert, xia2 is your friend in cases like this. This program is a real boon for the lazy crystallographer. All you need to type is: xia2 -3d /path/to/images and xia2 will automagically index, integrate and scale all of the sweeps together. Add the "-atom Se" flag (atom name as appropriate)

Re: [ccp4bb] discontinuous data wedges in XDS

Klaus Futterer schrieb: Is it not sufficient to first integrate the one wedge, then use this wedge as a reference data set when integrating the second one? (REFERENCE_DATA_SET= ../wedge01/XDS_ASCII.HKL) Klaus no, the REFERENCE_DATA_SET (first wedge of data) would then not be merged with the

[ccp4bb] Postdoctoral position in structural biology at Department of Medicinal Chemistry, University of Copenhagen

For more information please follow link: http://www.farma.ku.dk/index.php?id=3723 &tx_ttnews[tt_news]=291&tx_ttnews[backPid]=3650&cHash=2c3ad8912e information on research g

Re: [ccp4bb] discontinuous data wedges in XDS

Is it not sufficient to first integrate the one wedge, then use this wedge as a reference data set when integrating the second one? (REFERENCE_DATA_SET= ../wedge01/XDS_ASCII.HKL) Klaus - Klaus Fütterer,