RE: [PyMOL] set sphere_transparency?
Jason, The problem is that your script is changing the setting for the specific object-state by passing it an explicit object name and state number. cmd.set( sphere_transparency, str(val), spheres, 0, 1, 1 ) As an important compatibility consideration, I recommend for all API functions that you only ever pass the specific arguments you need to pass to API functions, and no others. In this case, I think that would be: cmd.set( sphere_transparency, str(val)) which simply changes the global sphere_transparency setting. That would then make it possible for a subsequent: set sphere_transparency, 0 To have the effect you expect. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jason Vertrees Sent: Tuesday, April 13, 2004 10:28 PM To: PyMol Users List Subject: [PyMOL] set sphere_transparency? Hey folks, Is this a bug or my incorrect usage of PyMol? (Using 0.95 on a Dual 64-bit Opteron SuSe 9.0 system.) I used this script (http://vertrees.org/~tree/fade_out.py) to create some images for a my first super-simple movie (http://vertrees.org/~tree/output.mpeg). The image (http://vertrees.org/~tree/bad_spheres.png) is the last image the script creates. The problem is that set sphere_transparency, 0 doesn't seem to work after my script is run. (The bad_spheres.png above show the command and resulting PyMol model/state.) So the bad_spheres.png file doesn't respond to 'set sphere_transparency, 0'. I'm a novice at PyMol and Python scripting, so I'm sure this is my fault instead of PyMol's. I've tried new selections, enable/disabling things and whatnot. Still sphere's refuse to play nicely. Oddly enough, 'hide spheres' works well. I've also 'mclear'ed and more. Any ideas? Thanks! -- Jason -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu --- 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] selecting atoms with PROview
I'm using PROView (I believe it's a PyMOL-enhanced tool) on a Windows 2000 machine, and was trying to pick some atoms in the structure window, but there is no visual indication of the selection. I tried it on a WinXP, and there were some visible pink dots showing up following my clicks. Have others encountered the same problem? Is it a Win2000-specific problem? -IJR _ The new MSN 8: smart spam protection and 2 months FREE* http://join.msn.com/?page=features/junkmail
[PyMOL] Re: give unique chain identifiers
Hi Warren, OK, that works just as you say it does. however, what I really need is each chain to have a unique chain identifier in the pdb file written out. I see there might be a problem here as there are 60 molecules, and only 24 letters in the alphabet I actually only want to have 15 of them in my model, so we could get round it that way, by deleting the ones I dont want but then how to give them unique pdb chain identifiers? I want to load the 15 molecule model in Bodil to do my actual modelling. cheers Dan On 6 Apr 2004, at 21:36, Warren DeLano wrote: 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 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] Selections
Master Users, I'm a bit new to PyMol and still trying to master selections. I've read the documentation and played with quite a few macromolecules now and still have some problems with selections. For example, I found a PDB online called 'pope.pdb' (a cool lipid bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to select all the hydrophobic tails and hydrophilic heads so that I may apply different attributes to each. If I need to select the tails, which in the PDB are labeled from C10 (or so) to C50 depending on the molecule, can I use something like c10-c50 (experience tells me no) or must I do c10+c11+c12...c50? So, it comes down to: do you prefer the macro method or standard; and, do you have any hints or tips for more accurate or powerful selections? As an example, how could I select just the tails or just the heads in the aforementioned pope.pdb file? Thanks. -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu
