Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

2013-07-29 Thread Dmitry Rodionov
Dear Sergei, IMO, the easiest way to achieve your goals is good old NIS and NFS with a centralized server on wired gigabit network. You could go with LDAP instead of NIS, but it is considerably more difficult to set up. One computer would act as a server, containing the user database, homes and

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

2013-07-29 Thread Dmitry Rodionov
o "setup" a new workstation by simply adding it to > your dhcp.conf on the server... > > All the best, > Georg > > > > > > > Am 29.07.2013 15:38, schrieb Dmitry Rodionov: >> Dear Sergei, >> >> IMO, the easiest way to achieve

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

2013-07-31 Thread Dmitry Rodionov
We don't have any performance/ reliability issues with our cheapskate setup either. Make sure the network is wired with Cat5e or Cat6 cables, especially if distances are 8m+ Dmitry On 2013-07-31, at 7:36 AM, Kay Diederichs wrote: > I have a very different experience with NFS: we are us

[ccp4bb] Conflicting Qt on OS X 10.6

2013-10-28 Thread Dmitry Rodionov
Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework

Re: [ccp4bb] Conflicting Qt on OS X 10.6

2013-10-28 Thread Dmitry Rodionov
lity version 4.8.0, current version 4.8.4) > > If you have $DYLID_LIBRARY_PATH set, try unsetting it. > > > > On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov wrote: > >> Good day! >> >> I'm having problems with qtrview (on OS X 10.6): it crashes or hangs

[ccp4bb] Dealnig with O-linked mannose

2013-11-20 Thread Dmitry Rodionov
Good day! I am refining what appears to be O-mannosylated protein structure. In my hands Coot (0.7.1) does not form the SER-MAN bond automatically. I made a SER-MAN.cif with jLigand, which takes care of the glycosidic bond. However, now the peptide bonds are not made to this custom residue (sam

Re: [ccp4bb] Dealnig with O-linked mannose

2013-11-21 Thread Dmitry Rodionov
Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond be

Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose

2013-11-22 Thread Dmitry Rodionov
> also make a script to do this. This is what I did during the time LINK > records were not properly handled by coot, refmac and buster. > > Best regards, > Herman > > > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.U

Re: [ccp4bb] Protein concentration form chromatograms

2014-01-15 Thread Dmitry Rodionov
If using Unicorn, 1)Open your chromatogram in Evaluation window. 2)Go to Operations-> Pool 3)Choose which baseline estimation suits you, define the pools (numbered rulers that appear under the chromatogram) 4)type in the path length (2 or 10 mm for UV-900 and 2 mm for UPC-900) 5)type in the mass

Re: [ccp4bb] PyMol and Schrodinger

2014-04-23 Thread Dmitry Rodionov
Hi Mirek, If you happen to be using OS X, Fink makes it very easy to install recent open-source pymol. Best regards, Dmitry On 2014-04-23, at 11:43 AM, "Cygler, Miroslaw" wrote: > Hi, > I have inquired at Schrodinger about the licensing for PyMol. I was surprised > by their answer. T

Re: [ccp4bb] project and literature organization software (laboratory information management software)

2014-05-06 Thread Dmitry Rodionov
Hi Tobias, We use LabTrove: http://www.labtrove.org/ Pros: Relatively easy local install Revision control Ability to attach any file Cons: clumsy blog formatting does not lay eggs. Regards, Dmitry It is a bit clumsy being based on a blog engine and does not lay eggs… But it works fin

Re: [ccp4bb] CCP4 update 6.3.0 006

2012-10-13 Thread Dmitry Rodionov
Hi Ben, Applications launched from Finder and Spotlight get environment variables from ~/.MacOSX/environment.plist (before 10.8) their own Info.plist (10.8) and launchd (system-wide) and not .tcshrc etc. Sounds like to get the updater to work from Finder for all users you have to set your $CCP

Re: [ccp4bb] Stabilization of crystals and ligand exchange

2012-10-18 Thread Dmitry Rodionov
Hi Sabine, Glutaraldehyde crosslinking worked pretty good for various soaks in my experience. J. Appl. Cryst. (1999). 32, 106-112[ doi:10.1107/S002188989801053X ] A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography C. J. Lusty Best regards,

Re: [ccp4bb] model protein for ligand soaking

2012-11-09 Thread Dmitry Rodionov
Hi Uli, I think Proteinase K and PMSF should work, though I never tried. Cheers, Dmitry On 2012-11-09, at 9:12 AM, Ulrich Zander wrote: > Hi All, > > > For a tutorial, we would like to demonstrate the method of ligand soaking in > protein crystals. I am thinking about using some sort of na

Re: [ccp4bb] hkl2000 install

2012-11-13 Thread Dmitry Rodionov
I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: > Dear everyone: > > I have got the returned "cr_info.dat&

Re: [ccp4bb] hkl2000 install

2012-11-13 Thread Dmitry Rodionov
r > > e-mail: mbfro...@post.tau.ac.il > Tel: ++972-3640-8723 > Fax: ++972-3640-9407 > Cellular: 0547 459 608 > > On Nov 13, 2012, at 18:12 , Dmitry Rodionov wrote: > >> I believe cr_info should go in /usr/local/hklint along with site files. >> It does not h

Re: [ccp4bb] Convert cbf to png/tiff?

2013-01-10 Thread Dmitry Rodionov
I think ADXV will do the trick. Regards, Dmitry On 2013-01-10, at 3:36 PM, Frank von Delft wrote: > Hello all - anybody know an easy way to convert CBF images (Pilatus) into > something lossless like tiff or png? > > Ideally *easy* as in r e a l l y e a s y and not requiring exten

Re: [ccp4bb] Mac mini advice

2013-01-22 Thread Dmitry Rodionov
AFAIK there is no problem mixing and matching different timing RAM: system will run at the speed of the slowest module. I don't think anybody will notice the difference with CAS latency Coot'ing and Refmac'ing. I don't think there is much sense in having more than 4 GB of RAM per physical core

Re: [ccp4bb] Mac mini advice

2013-01-23 Thread Dmitry Rodionov
We have 10.5&10.6 servers and briefly tested 10.7 server. Last time I tried, Ubuntu 12.04 box would not authenticate users registered on the OS X Open Directory server. Before that, 10.04 clients would cause random user lockouts. NFS GUI is gone as of 10.7 Regards, Dmitry On 2013-01-23,

Re: [ccp4bb] Off-topic: Fungal growth in robot trays

2013-03-13 Thread Dmitry Rodionov
8. Empty the carboy and fill the supply lines and wash stations with 20% ethanol at the end of the day. (Requires decontamination in this case) Best regards, Dmitry On 2013-03-13, at 10:04 PM, Viswanathan Chandrasekaran wrote: > Dear All: > Thank you for your responses. Here is a su