Re: [ccp4bb] crystallization plates and robotics

Dear CCP4BB'ers, I have received many responses to my inquiry on MRC 2-well plates and liquid dispensing robots. I also got many messages (and phone calls) from product vendors, and received a batch of the latest MRC plates from Swiss-Ci, the original manufacturer of this plate. This latest b

Re: [ccp4bb] program to display space group symmetry in three dimensions

On Tue, 16 Mar 2010 20:11:29 -0400, Karthik S wrote: >Hi, I was looking around for programs that display space group symmetry >information and could not find any but perhaps i am lost for valuable or >relevant keywords. >I found two references TABLES and CRYST, but are there other alternatives >t

Re: [ccp4bb] program to display space group symmetry in three dimensions

Hi Karthik, you can use this: http://cci.lbl.gov/servers/cctbx/explore_symmetry.html and you may find this useful too: http://cci.lbl.gov/servers/index.html Pavel. On 3/16/10 5:11 PM, Karthik S wrote: Hi, I was looking around for programs that display space group symmetry information and c

[ccp4bb] program to display space group symmetry in three dimensions

Hi, I was looking around for programs that display space group symmetry information and could not find any but perhaps i am lost for valuable or relevant keywords. I found two references TABLES and CRYST, but are there other alternatives that are more recent, or that can run on more common hardware

[ccp4bb] Equation for combining measurements

Dear Crystallographers, A basic question: what is the equation currently used to combine/merge multiple measurements of I and sigI? (Or a reference would be fine as well (or maybe better.)) Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern Un

Re: [ccp4bb] how to make covalent bond between ligand and protein residue in coot?

On Mar 16, 2010, at 9:32 AM, Paul Emsley wrote: Coot needs to be told about the geometry of the link so that it can refine it. Why wouldn't it be sufficient for Coot to approximate/guess these parameters for the purposes of building? No one is going to do an all- atom refinement of their

[ccp4bb] Project deletion bug?

Only projects near the top of the projects list (first dozen or so?) can be deleted from the project directory task window using the mouse right-click. This only happens when there is a large number of projects stored in CCP4i. Also, the project directory window cannot be resized in 6.1.3. I'm

[ccp4bb] patch to ARP_wARP 7.1

Dear All, Following very useful feedback, we have made a patch #1 to ARP/wARP version 7.1, which addresses the following issues: CCP4i GUI and command line module 'ARP/wARP solvent': 1. Assignment of Rfree 2. Reference to the log file containing the error message CCP4i GUI and command line mo

[ccp4bb] asking for less "red tape" for European research funding

Dear fellow cristallographers, It has come to my attention that there is a petition at the moment, directed at the *European Council of Ministers and the Parliament, asking for less "red tape" and cumbersome financial regulations from the EU concerning European research funding.* http://www.

Re: [ccp4bb] how to make covalent bond between ligand and protein residue in coot?

herman.schreu...@sanofi-aventis.com wrote: I, and probably many coot users, would appreciate it very much if you could add a "create covalent link" option in coot instead of having us wade through 8 pages of instructions and hoping that we put exactly the right number of space characters in the l

Re: [ccp4bb] iodine density

Hello, the guess about ripples is most likely correct. Just do this simple experiment: place one iodine in a middle of a cubic box and compute F-calc map. You will see mazing picture! At least I enjoyed. You will see a number of concentric shells of density around iodine, positive and neg

[ccp4bb] FW: [ccp4]: Job Posting

Dear all, Please see the attachment for a new job advertisement for Research Associate/Senior Research Associate - Biophysics/Biochemical Pharmacology in Genentech. Applicants should apply directly on Genentech website. In case a submission email address is necessary, please respond to: genente

Re: [ccp4bb] iodine density

I am going to try to guess in this one. As you say, the positions of the iodines cannot be challenged. But maybe their occupancies can. Is there anomalous signal from iodine at your wavelenght? Are you expecting radiation damage? In any case: I see a spherical shell of low density around each one o

[ccp4bb] OT: NMR postdoctoral position at HSR, Milano

Please find enclosed the ad for a postdoctoral research position in the NMR lab headed by Giovanna Musco at the San Raffaele Scientific Institute, Milano (Italy). Note that enquiries should be sent to directly to Giovanna Musco (musco.giova...@hsr.it ). Best, Marina annuncio_biophy

Re: [ccp4bb] arp/warp

Dear Rafael, We have seen this already twice, it is a bug, sorry. The fix is being made and, when ready within a day or two, we will announce it. With best regards, Victor Rafael Counago wrote: Dear all, I am getting an error message when I run arp/warp using CCP4i. */"QUITTING ... ARP/w

Re: [ccp4bb] arp/warp

Dear Raphael and others who experienced this, in some rare cases we have seen that the 'restraints' module of ARP/wARP can have a malfunction. If this is the case for your data, then the best you can do at the moment - while the fix is not there - is to deactivate the use of this module in the

Re: [ccp4bb] arp/warp

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The other possibility you might need to consider is wether or not you have java running on your machine. "restraints" is in java, and it seems that ARP/wARP stops just when starting restraints. As for the "error" message you're seeing, it is well

Re: [ccp4bb] arp/warp

Dear Rafael, dear Li Chan, is this the first time you run arp/warp on that particular computer? Maybe the architecture of the binaries are not the correct ones. You might search for the 'snow' binary (which leaves the empty log file) with the command 'find ./ -name snow' issued from the arp/warp

Re: [ccp4bb] how to make covalent bond between ligand and protein residue in coot?

Dear Paul, I, and probably many coot users, would appreciate it very much if you could add a "create covalent link" option in coot instead of having us wade through 8 pages of instructions and hoping that we put exactly the right number of space characters in the link record. Best regards, Herman

Re: [ccp4bb] arp/warp

Hi all, I got the same errors as Rafael. Please help. Thanks Peter > Date: Tue, 16 Mar 2010 14:39:10 +1300 > From: rafael.coun...@otago.ac.nz > Subject: [ccp4bb] arp/warp > To: CCP4BB@JISCMAIL.AC.UK > > Dear all, > > I am getting an error message when I run arp/warp using CCP4i. > >

Re: [ccp4bb] Correct MR solution

Dear Bob, I am quite puzzled by the results you describe. Here are some of my questions/comments: - You could index in P2 and in P222. I assume you have in both cases the same cell dimensions and for P2 beta very close to 90°? - How do the diffraction images look like? I would check every 30°