[ccp4bb] Seeking Linux experts' adivice

Hi, All, After lunching pymol, if I drag the Xterm window produced by PYMOL using mouse, my computer will suddenly freeze, the keyboard seems no longer functioning. The only thing I can do is to re-boot my Linux system. This problem makes it almost impossible for me to use PYMOL on my LINUX

Re: [ccp4bb] pymol movies scripts

I used to do that in POVray. you can use any program that writes POV output and can generate all the objects you want. I used to write each object I want to manipulate to a separate file and #declare ed it as a POVray object. Then I wrote a 'master' povray file, that #include d the aforementioned o

Re: [ccp4bb] REFMAC and Hetroatoms

Dear Vineet, It seems, in your input PDB file the atom level for CA and CL in the last column is C. It should be CA & CL respectively. The atom name in the input file and Dictionary doesn't match. all the best Manish Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all i am having Ca2+ and Cl

[ccp4bb] phaser and percent composition result [ part 2]

i wrote "(ensemble) / (sequence)" to get a percent composition i forgot to emphasize that i do not mean the Vm or the "Z" composition, but the composition as one would enter e.g. COMPosition ENSEmble mol1 FRACtional 0.22 or COMPosition SCAttering -bryan

[ccp4bb] phaser and percent composition result

the phaser docs/tutorial indicate that phaser calculates what could be called "(ensemble) / (sequence)" to get a percent composition, however i cannot seem to find the direct result from this in any output (.sol, .sum, .pdb, .log... other?) any tips appreciated as to if this can be found / whe

[ccp4bb] Postdoc Position in Protein Crystallography

POSTDOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY An NIH-funded POSTDOCTORAL position is available immediately to study the structure and function of (1) ATP-dependent molecular machines [e.g. Cell (2003) 115:229; Mol. Cell (2007) 25:261] and (2) multi-component protein assemblies [e.g. EMBO J.

[ccp4bb] REFMAC and Hetroatoms

Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refinement with REFMAC i m getting following warnings: I am reading library. Please wait. mon_lib.cif WARNING : residue: CA994 chain:XX different element name: file:"C "

Re: [ccp4bb] pymol movies scripts

Go to the Pymol community wiki (www.pymolwiki.org) and install SLERPY, a python plugin that allows you to create multiple scenes and transitions in Pymol. It is possible to create some pretty sophisticated animations using slerpy, including fading transitions of surfaces. If you ray-trace the m

Re: [ccp4bb] arp/warp in p22121

Dear Florian, ARP/wARP supports 65 space groups where proteins crystallise and it indeed uses the Hermann-Mauguin convention as given in the International Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is not supported by ARP/wARP. The standard for it would be number 18, P

Re: [ccp4bb] arp/warp in p22121

Hi - ARP/wARP only likes standard space groups, like P21212, P22121 is not-standard ... oh well ... (Eleanor is complaining about it for about 13 years ... but never mind that she is right) Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i). Choose 'Entering reflection tr

[ccp4bb] arp/warp in p22121

Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says "this space group is not supp

[ccp4bb] pymol movies scripts

Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For instance, I'd love to generate a movie

Re: [ccp4bb] Rotation Axis visualisation.

Hello David, In CCP4mg you can display any arbitrary vector in a variety of display styles - there is an example in the the online documentation: http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/vector.html Liz On Tuesday 18 September 2007 10:00, David Briggs wrote: > Good morning ccp4bb-ers! >

[ccp4bb] phase seapration

Hi, i am trying to crystallize a protein. i got phase separation in many conditions. can anybody tell me about phase separation? Is this good or not? My protein concentration is 17mg/ml. shall i increase it? Thanks in advance. parveen

[ccp4bb] Rotation Axis visualisation.

Good morning ccp4bb-ers! I have two protein-protein complex structures, and the orientation of one of the components shifts slightly with respect to the other component between the two structures. If I run superimpose on the shifting component I get this: CROWTHER ALPHA BETA GAMMA 12.41607