Re: [ccp4bb] Zalman ZM-M215W and ZM-M240W with coot and pymol
I find the 22 sufficient if run at highest resolution 1680x1050. If you really need more space get a second one and run the machine in dual mode. I'm waiting for Apple to announce finally the new MacPro's to get one of them. It will be connected to a 24 Cinema Display and a 22 Zalman. Jürgen - 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/ On Jul 15, 2010, at 7:52 PM, Engin Ozkan wrote: On 7/13/10 11:05 AM, Daniel Lietha wrote: Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in 3D with Coot and Pymol (would use them on Mac OS10.6)? If so, does the increased resolution improve things compared to the ZM-M220W? Thanks, Daniel Let me bring back to life the thread Daniel started two days ago. Do any of the Zalman monitors related to ZM-M220W work with coot and pymol in stereo mode (for linux)? We are looking for as large a monitor we can buy, and at least one lab member finds it an offense to even consider buying a 22-inch monitor. In the age of huge flat display TVs, it appears that one cannot force others to look at small screens (somehow smartphones are an exception to this). We can definitely use extra space on the monitor when we have all those pymol, coot, ccp4i and phenix GUIs on, but we also want the stereo option possible for that rare event. Thanks, Engin -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] Question about R/Rfree value difference
Something else to consider is what is your space group ? P212121 but truly P21 with twinning fraction close to 0.5 ? That's one of my recent cases. 1.9 Å data beautifully refined built but the Rwork/Rfree gap was 13 percent. After changing the space group and applying the twin law the gap is 3 percent 18.4 and 21.3 Jürgen - 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/ On Jul 8, 2010, at 1:17 AM, Sampath Natarajan wrote: Dear all, I have a question about the R free value. I refined a structure with 2A resolution. After model building and restraint refinement using Refmac program, the average B factor was around 50 for all atoms. The R/Rfree were around 22/34. Then used the TLS refinement choosing entire molecule. Then R/Rfree reduced as 20/32. But the average B factor was reduced as 30. The R/Rfree difference is about 12% in final refinement. I feel it is significantly higher. Could any one suggest me to reduce the Rfree value more? or is it good to submit the data in the PDB database with this 12% difference? Thanks for the suggestions. Sincerely, Sampath N
Re: [ccp4bb] CCP4 on iMac
See and follow the rules on this web site: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OS_X Jürgen - 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/ On Jun 16, 2010, at 12:59 PM, Hari Namboodiri wrote: Hello CCPeers, I am trying to download CCP4 and Coot on to my new Mac( Mac OSX 10.6.3). On the downloading site, I am seeing couple of files, which are the ones to be downloaded? I tried to download the intel,dmg. But it did not launch ccp4. Are there any other files to be downloaded? Tcl/Tk etc? Regards, Dipta
Re: [ccp4bb] Characterization of Protein Conformational Changes
You can abuse/mis-use the TLSMD server from Ethan to analyse domain movements and draw your conclusions accordingly, see here http://skuld.bmsc.washington.edu/~tlsmd/ Jürgen On 7 Jan 2009, at 16:54, Jacob Keller wrote: Dear Crystallographers, I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call mobile. Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least- squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
Re: [ccp4bb] Mac pro
Hi Sheemel, I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. Jürgen On 6 Jan 2009, at 06:27, Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
