Re: [ccp4bb]: Re: [o-info] Q&A O graphics description language

[Vaheh Oganesyan]

Here are the replies I got for question on sym_sphere command in chronological order: 1. from [EMAIL PROTECTED]    how about using coot...? (not sure if it doens this exactly) 2. from [EMAIL PROTECTED] I think what you are looking for can be accomplished with XPAND from the Uppsala Software Factory thanks to Gerard J. Kleywegt and friends... http://alpha2.bmc.uu.se/usf/ 3. from Gerard have a look at XPAND - http://xray.bmc.uu.se/usf/xpand_man.html - i think it may do what you want to do (e.g., options A, B or E) 4. [EMAIL PROTECTED] suggested to have a look at scripts from Simon Lovell and J. Michael Word From the Richardson's lab 5. [EMAIL PROTECTED] mentioned that such a feature has been requested a while ago and version of 'O' capable of doing it already exist. 6. Alwyn promised to make that version of 'O' publicly available in the next release. Thank you, all. -Vaheh Vaheh Oganesyan wrote: Hello All, When using sym_sphere command 'O' initially shows only residues within the specified radius from the current center. I am trying to write out only those residues, but noting seems to work, whole molecule is being written out. The only way I found is the trivial range determination in s_a_o or pdb-wr commands, which have noting to do with sym-sphere or sphere_cen and is very elaborate. Does 'O' actually creates a data block that contains only close portion of symmetry mates? If so, I will appreciate if someone can tell the name of it. Or may be there is a prog. in CCP4 that I am not aware of that can take the current molecule and using the symm. information generate a coordinate file with all close contacts. Programs ncont, pdbset, contact, act and distang will not do it. That info will be appreciated as well. Thanks. Vaheh.

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