[PyMOL] Re: split_states
Warren, Exactly what I needed! cheers Dan On 5 Apr 2004, at 23:08, pymol-users-requ...@lists.sourceforge.net wrote: Message: 10 From: Warren DeLano war...@delanoscientific.com To: 'Todd Geders' ged...@purdue.edu, 'Ann Mullin' amul...@tulane.edu Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] biological unit question Date: Mon, 5 Apr 2004 13:07:13 -0700 Todd, Try MacPyMOL for the full PYMOL effect. http://delsci.com/macpymol There is also a new command in the 0.95 series: split_states object-name which will spread a PDB biological unit (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with all_states = 1. load 1c8e.pdb1, 1c8e split_states 1c8e delete 1c8e zoom spectrum b hide lines set cartoon_sampling,3 show cartoon bg_color grey70 set hash_max, 150 ray ... orient zoom complete=1 ray image screen-shot at: http://delsci.com/img/1c8e.jpg http://delsci.com/img/1c8e-screen.jpg Note that looking at large systems such as this (255300 atoms) may take some extra RAM -- 1.5 GB is recommended for this task, and it still takes a dual 2 Ghz G5 85 seconds to render... Cheers, Warren Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] problem in installation
Yes, i've had the same problem too. Jules On Mon, 5 Apr 2004, Tom Lee wrote: I have trouble installing PyMOL using pymol-0_95-bin-win32-py23.zip. Here is the message I got. The installer is unable to locate Python. Python must be installed before PyMOL. Do you wish to abort? I have Python2.3.2 installed, and there was no problem installing pymol_0.93 with this version of Python. Anyway, I reinstalled Python again, but it doesn't help. Does anyone have this problem? Tom Lee --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] save all not working for multiple objects from split_states?
Hi all, I opened a biological unit pdb file of a viral capsid protein containing the 60 states or models making up the whole viral capsid structure. I did split_states to get all 60 molecules as individual objects sweet! then I deleted the ones I didnt want, leaving 15 molecules around one of the 5 fold symmetry axes. now I want to save these molecules to a pdb file. so I did save 5fold.pdb, all this gave no errors, but the pdb file written only contains END what am I doing wrong? I expect it is my simple mistake? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] Delete atoms out of unit cell box
Is there an easy way to delete all atoms that fall outside of the unit cell after doing a symexp? I'm doing it by hand which takes too long and is error prone... Thanks in advance.
RE: [PyMOL] save all not working for multiple objects from split_states?
Dan, That's the not expected result, but indeed you have a problem -- each of those subunits will have identical atoms. To resolve this, assign a unique segment identifier to each subunit: load 1c8e.pdb1, 1c8e split_states 1c8e delete 1c8e alter all, segi = model[-4:] rewind save test.pdb, all dele all load test.pdb The reason why you were getting a PDB file with just END is that you didn't return the viewer ro frame/state 1 after moving all of the data to state 1. After the above, you'll now be able to address each subunit indepently as: hide show ribbon color red, segi 0001 zoom segi 0001 http://delsci.com/img/1c8e-subunit.jpg Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Daniel James White PhD Sent: Tuesday, April 06, 2004 6:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] save all not working for multiple objects from split_states? Hi all, I opened a biological unit pdb file of a viral capsid protein containing the 60 states or models making up the whole viral capsid structure. I did split_states to get all 60 molecules as individual objects sweet! then I deleted the ones I didnt want, leaving 15 molecules around one of the 5 fold symmetry axes. now I want to save these molecules to a pdb file. so I did save 5fold.pdb, all this gave no errors, but the pdb file written only contains END what am I doing wrong? I expect it is my simple mistake? cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (new mobile) NEW PHONE NUMBER!!! http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id70alloc_id638op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] (no subject)
Hi,everybody: Is there someway so that I can generate several asymmetry molecules from one asymmetry unit in pymol? Thank you. Xiaofeng _ Check out MSN PC Safety Security to help ensure your PC is protected and safe. http://specials.msn.com/msn/security.asp
