[ccp4bb] find water in refmac5

2009-08-07 Thread Elad Binshtien
Dear all, I am using Refmac_5.5 in win OS. in the  linux version ther is a option to asked the program to find a water (with coot i think) . how can i do it in the win version? Thank you in advance for your any helpful suggestions.  Best, Elad Elad Binshtein Ph.D student Department of Li

[ccp4bb] Postdoctoral associate position at MacCHESS

2009-08-07 Thread Marian Szebenyi
Post-doctoral Associate - Biological Small-Angle Solution Scattering Cornell High-Energy Synchrotron Source The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) has an opening for a post-doctoral associate. Applicants should have a Ph.D. degree in a f

[ccp4bb] cheap/useful alternatives to bloatware

2009-08-07 Thread Patrick Loll
Hi, This is off-topic in the sense that it's not about reciprocal space, but graphics ARE an integral part of publishing and teaching... I just upgraded to Leopard*, and find that my versions of Photoshop & CorelDraw no longer work. I can't stomach spending big bucks for the new version

[ccp4bb] Postdoctoral position at MacCHESS - CORRECTION

2009-08-07 Thread Marian Szebenyi
Note - the job notice posted earlier had an incorrect address to send applications to. Here is the correct notice: Post-doctoral Associate - Biological Small-Angle Solution Scattering Cornell High-Energy Synchrotron Source The Macromolecular Diffraction Facility of the Cornell High-Energy Synch

[ccp4bb] TLS restrained refinement

2009-08-07 Thread ManojSaxena
Hi, I am using Refmac 5 for refinement of my protein model (solution by molecular replacement) with TLS restrained refinement option on.Can anyone please guide me about the parameters settings for TLS.I have used defaults .Wether it is good to use multiple TLS restrained refinements rounds.

[ccp4bb] cryoEM maps out of scale for docking experiments

2009-08-07 Thread Filip Van Petegem
Hello all, While trying to perform some docking experiments with crystal structures into cryoEM maps, I found that some deposited EM maps are not at the right size relative to crystal structure coordinates (e.g. a ccp4 formatted deposited EM map looks smaller than a crystal structure that's suppos

Re: [ccp4bb] cryoEM maps out of scale for docking experiments

2009-08-07 Thread Daniel Anderson
(This question is repeatedly asked.) Replace the "unit cell" parameters in the EM map file, like this: mapman -b mapsize 820 << eof read m1 bigmap.ccp4 ccp4 cell m1 749.8 749.8 749.8 90 90 90 write m1 smallmap.ccp4 ccp4 quit eof (for completeness, mapman originates in http://xray.bmc.uu.se/

[ccp4bb] how to generate the figure of buried surface area

2009-08-07 Thread Jiamu Du
Dear all, I am analyzing a complex structure and generate figure using the program Pymol. Here I want to generate a figure to show the buried surface area. How to generate this type figrues? Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemi