Re: [ccp4bb] Please Delete: FW: Departmental License for Pymol

W236 lab: CIS W229 website: http://ejadamslab.bsd.uchicago.edu Office phone: 773-834-9816 Lab phone: 773-834-0660 Department Fax: 773-702-0439 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr

Re: [ccp4bb] Superposition of electron density

to superimpose several structures together with their electron density to show the presence of point mutations. Is there any possibility to superimpose the electron density together with its structure or to translate/rotate the electron density alone? Thanks you, Jan -- Jason Vertrees, PhD Director

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically

Re: [ccp4bb] Off-topic PyMOL Issue

! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- Jason

Re: [ccp4bb] GeForce Graphics cards

restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] GeForce Graphics cards

. Cheers, -- Jason On Wed, Feb 13, 2013 at 3:15 PM, S K alek6...@gmail.com wrote: Hi Jason, aren't the current gaming monitors all (or mostly) 120 Hz? At least companies like alianware sell GeForce together with 120 Hz monitors. A On Wed, Feb 13, 2013 at 4:02 PM, Jason Vertrees

Re: [ccp4bb] 3D alignment of points (atoms)

-- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 On Fri, Dec 28, 2012 at 5:53 AM, Tom Oldfield oldfi...@ebi.ac.uk wrote: Hi In you post you say you want to fit a small number of points. Note

Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom

/Selection_Algebra). Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] Efficient way of showing residue conservation

into PyMOL on that page. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] Mac OSX 10.7 Lion

Phil, On Fri, Sep 9, 2011 at 4:28 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I upgrade? MacPyMOL works fine on Lion. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger

Re: [ccp4bb] structure based superposition

* -- http://www.pymolwiki.org/index.php/Fit Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] Pymol question

Hi Chris, set cartoon_side_chain_helper=1, HISA should be set cartoon_side_chain_helper=1 That setting cannot yet be applied just to a specific set of atoms: it's a global setting. This is something we should add to our to-do list. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product

Re: [ccp4bb] PDB data mining

% bb.index))) cmd.delete(n) f.close() print Processed %d files. Please see %s for results. % (len(files), outFile) Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] help with pymol error message

that reads map or brick objectname of my file not found. I can however open the entire density which tells me i have the file loaded correctly. My map file is a .ccp4 file. I do put in .map suffix when typing in the command. Any help will be welcome. Thanks in advance Rakesh -- Jason

Re: [ccp4bb] Graphics for notebook

doing anything graphics related, I'd highly suggest moving away from integrated boards. Last, the integrated mobile boards are the worst offenders--I'm looking at you Intel GM945!--so if you can help it, stay away from them. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger

Re: [ccp4bb] pyMol--set up view through one axis of the unit cell

of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] local copy of wiki

(GNU/Linux) iD8DBQFMbkWEUxlJ7aRr7hoRAhm2AJ0akHmmT8mUJUhF+Ivap1Ae32LhfgCgpezU osMfrFB+I8/teK2u+w4wQuw= =sj7e -END PGP SIGNATURE- -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Jason Vertrees

Re: [ccp4bb] CONE built-in in pymol

) iD8DBQFMbQ6ZUxlJ7aRr7hoRAoxnAKC900VnP+FAVmL89jWtNB6xosFD5ACeJx4C XioMtnyCI2F6D7VOsQI07V8= =GFYk -END PGP SIGNATURE- -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] merging Pymol sessions ? Non-CCP4 question

Lab:  +1-410-614-4894 Fax:  +1-410-955-3655 http://web.mac.com/bosch_lab/ -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] How to show the ligand in my protein as sticks....???

. Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [ccp4bb] How to show the ligand in my protein as sticks....???

proper bonding, especially in things like heme groups: you might have to do some bond-editing yourself. Good luck, -- Jason On Mon, Apr 12, 2010 at 3:14 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear Jason Vertrees, My ligand is a metal complex. i followed the way u suggested to me

Re: [ccp4bb] Zalman LCD availability

Andrew, My Zalman Trimon is in the mail. It was ordered about a week ago, so no issues here. I am discussing 3D PyMOL development with Zalman support and can ask them about it if you like. -- Jason P.S. First post. :-) -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e