[ccp4bb] How to run Java program?
Hi,
I have a java program named Switch.java, I want to run it under fedora5
core, I donnot know any compiler
I need to install? I installed a package named jre-1_5_0_11-
linux-i586-rpm.bin, when I use command
java Switch.java
wrong information came out:
Exception in thread main java.lang.NoClassDefFoundError: SwitchI
at gnu.java.lang.MainThread.run(libgcj.so.7)
Caused by: java.lang.ClassNotFoundException: SwitchI not found in
gnu.gcj.runtime.SystemClassLoader{urls=[file:./], parent=
gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}
at java.net.URLClassLoader.findClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.Class.forName(libgcj.so.7)
at gnu.java.lang.MainThread.run(libgcj.so.7)
Then I used command yum install libgcj.so.7 , but it was not helpful.
I am a java newhand, any help will be appreciated, thanks!
[ccp4bb] Question about cryoprotectant
Hi, l have a crystal grow at condition screen l 40: 0.1M tri-sodium citrate dihydrate pH5.6 isoproponal 20%PEG4k 20% and the crystal need a cryoprotectant, we have used the 30% glycerol but it is not good, the mosaicity of the diffraction pattern is a little high, so anyone knows which is the best cryoprotectant for this crystal? Thanks!
Re: [ccp4bb] How to run Java program?
The file you need to run should end .class or .jar. If you don't have
such a file, you'll need to compile it first. You probably need a java
sdk rather than jre, although gcj might do the trick.
Then:
javac Switch.java
should make the .class file. (You may need to include the path to your
java compiler).
Finally:
java Switch.class
should run it.
Of course Switch may not be a runnable class, in which case you'll get
an error.
Kevin
yang li wrote:
Hi,
I have a java program named Switch.java, I want to run it under
fedora5 core, I donnot know any compiler
I need to install? I installed a package named
jre-1_5_0_11-linux-i586-rpm.bin, when I use command
java Switch.java
wrong information came out:
Exception in thread main java.lang.NoClassDefFoundError: SwitchI
at gnu.java.lang.MainThread.run(libgcj.so.7)
Caused by: java.lang.ClassNotFoundException: SwitchI not found in
gnu.gcj.runtime.SystemClassLoader{urls=[file:./],
parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}
at java.net.URLClassLoader.findClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7 )
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.Class.forName(libgcj.so.7)
at gnu.java.lang.MainThread.run(libgcj.so.7)
Then I used command yum install libgcj.so.7 , but it was not helpful.
I am a java newhand, any help will be appreciated, thanks!
Re: [ccp4bb] How to run Java program?
Kevin Cowtan schrieb:
The file you need to run should end .class or .jar. If you don't have
such a file, you'll need to compile it first. You probably need a java
sdk rather than jre, although gcj might do the trick.
Then:
javac Switch.java
should make the .class file. (You may need to include the path to your
java compiler).
Finally:
java Switch.class
should run it.
Of course Switch may not be a runnable class, in which case you'll get
an error.
Kevin
yang li wrote:
Hi,
I have a java program named Switch.java, I want to run it under
fedora5 core, I donnot know any compiler
I need to install? I installed a package named
jre-1_5_0_11-linux-i586-rpm.bin, when I use command
java Switch.java
wrong information came out:
Exception in thread main java.lang.NoClassDefFoundError: SwitchI
at gnu.java.lang.MainThread.run(libgcj.so.7)
Caused by: java.lang.ClassNotFoundException: SwitchI not found in
gnu.gcj.runtime.SystemClassLoader{urls=[file:./],
parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}
at java.net.URLClassLoader.findClass(libgcj.so.7)
at java.lang.ClassLoader.loadClass(libgcj.so.7 )
at java.lang.ClassLoader.loadClass(libgcj.so.7)
at java.lang.Class.forName(libgcj.so.7)
at gnu.java.lang.MainThread.run(libgcj.so.7)
Then I used command yum install libgcj.so.7 , but it was not helpful.
I am a java newhand, any help will be appreciated, thanks!
java Switch
will run it. Withut the .class
Re: [ccp4bb] Question about cryoprotectant
Dear Yang Li, Cryoprotection of crystals is not an exact predictive science - you have to try a number of things, and in the worst case scenario, none of the stuff you try may work out. Assuming that your crystals are OK to start with (capillary mounted room temp. pattern would confirm that), you can explore a whole wide range of cryoprotectants. I am slightly surprised that you need one at all - at 20% isopropanol together with 20% PEG you have 40% organic content which is usually enough for glassification. You may want to explore the actual cryo-mounting method - there are several options for flash freezing and they're not all the same in terms of results. Assuming that you do really need cryoprotectant, you may want to experiment with addition of EG or glycerol, etc. right into the mother liquor when you set things up - this way, if the crystals grow they're already protected and ready to go. If you can somehow get rid of isopropanol, your life would be easier as well because this alcohol is very volatile which can cause no end of trouble when working with crystals in the open air (among other things, they tend to 'zoom' around the drop as the surface of the drop is pulled around by fluxes of evaporating iPrOH. There are numerous other things you can try, including the one mentioned here: http://www.xtals.org/ under 'stuff'. Regards, Artem Hi, l have a crystal grow at condition screen l 40: 0.1M tri-sodium citrate dihydrate pH5.6 isoproponal 20%PEG4k 20% and the crystal need a cryoprotectant, we have used the 30% glycerol but it is not good, the mosaicity of the diffraction pattern is a little high, so anyone knows which is the best cryoprotectant for this crystal? Thanks!
[ccp4bb] Reseach Associate position
Dear All, Please pass the following advertisement on to anyone you think might be interested in this position. Thank you. With best regards, Dirk - - For our Oncology site Boehringer-Ingelheim Austria GmbH, Vienna we search a Research Associate in Medicinal Chemistry Job ID 277: Duties and Responsibilities: - crystallization of new proteins and protein-ligand complexes - maintenance of automated crystallization and imaging systems as well as of lab infrastructure - measurement of crystals at inhouse x-ray source - preparation of crystals for Synchrotron measurements - clear documentation of results in lab books and relevant databases Qualifications: - Masters degree, completed training as laboratory technician or equivalent - Several years practical laboratory experience are a must. - Sound knowledge of protein chemistry, good knowledge of chemistry, biochemistry and physics - Experience in protein crystallography would be advantageous. The successful candidate must be motivated, capable of working independently, and enjoy working in a collaborative setting. for more information, please visit: http://www.boehringer-ingelheim.at (Job/Karriere) [Laboranten im Bereich Biochemie (m/w) ]
[ccp4bb] Refinement of low resolution structures
Hi all, I'm refining the structure of a complex at low resolution (4.5). Certainly refinement at low resolution will become more common, but there isn't a whole lot out there now to use as a guide. I've incorporated most of the suggestions from DeLaBarre and Brunger, but I'm looking for any other suggestions and I have a couple of specific questions. I have independent, high resolution structures for both molecules of the complex, and I got a nice solution from Phaser. There is 4-fold NCS (45,000 atoms in the ASU). Because of the low resolution I have also added manual restraints based on secondary structure of the individual structures to help the observation/parameter ratio. So far, I have been using tight NCS restraints in Refmac along with Babinet scaling for bulk solvent, fixed B for the solvent, and isotropic refinement for B factors. Currently, R=25.7 Rfree=30.0 and the difference between R and Rfree has stayed pretty constant from starting values in the 40's. I just loosened up the NCS and got a fairly significant drop in R (21.3)but a less significant drop in Rfree (28.8). The maps seem somewhat better with some possible ion sites getting stronger in the difference map. Should I worry about the large R change relative to Rfree? I also have some very strong density for a portion of a molecule (missing in the original structure) that I can't model unambiguously at this resolution. It is very likely in multiple conformations. I'm guessing this is going to cause the R factors to bottom out and I'm worried trying to push the R factors down without building this will lead to a some distortion around this area. Any suggestions on how to handle this? Finally, what would you like to see in a paper as validation for the correctness of a model at this resolution and phased by MR? Omit maps of key features? Yes, I am trying to get higher resolution data. Thanks in advance. --paul -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 [EMAIL PROTECTED]
Re: [ccp4bb] pdb-l: Sequence Location in Protein Tertiary Structure
By the way, I'll extend that question: the validation software Verify3D assigns not only buried state but also polar fraction and secondary structure, using the probability of finding given residues in the different environment defined when combining all this information to calculate a score of protein regions, which could identify, for example, sequence misthreading. The program is rather old (1991) and, aside from the automated validation site at UCLA (which just let you upload a PDB and get the scores), I haven't found a web page for it. Is there available code to assign residues to one of those environments and updated probabilities of finding amino acids in each one? Lucas Wei Huang wrote: Hi all, Do someone know a tool which could identify the location of the sequence in tertiary structure known protein, that is the sequence is on the surface or in the core? Usually we use visualization tools, such as RasMol, VMD, to identify this by our eyes. But I don't know whether there are tools that we could input PDB file and the sequence only, then the computer tells us the sequence is on the surface or in the core. __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
