Re: [PyMOL] how to load two separate pdb files simultaneously

I made a mistake. I meant command-line pymol *pdb or pymol A.pdb B.pdb etc. Not load *pdb. Maia Cherney wrote: > Also you can use > > load A.pdb B.pdb C.pdb > > or load *pdb > > > > leila karami wrote: >> Dear all >> >> very thanks for your time

Re: [PyMOL] how to load two separate pdb files simultaneously

Also you can use load A.pdb B.pdb C.pdb or load *pdb leila karami wrote: > Dear all > > very thanks for your time and attention. > > my problem was solved by > load A.pdb > load B.pdb > > > --

Re: [PyMOL] [Fwd: Re: select residues from different chains]

Thanks, Zhijian It worked zjxu wrote: > Dear Maia, > Would you like to try this: > select bridge, (c. a and i. 160+356+505+507+508) or (c. c and i. > 275+355+128) > > Best Regards, > Zhijian Xu > > Maia Cherney wrote: >> Hi Jason, >> >> I keep se

[PyMOL] [Fwd: Re: select residues from different chains]

Hi Jason, I keep sending my e-mail from a wrong address that the pymol mailing list does nor recognize. I need a command that would allow me to select several residues from two chains, something like that: select bridge, /prot//A/160+356+505+507+508/+prot/C//275+355+128/ But I cannot find cor

Re: [PyMOL] hbs

Thank you, Marius. Yes, it does. Marius Retegan wrote: > Hello Maia, > > Does this work? > color black, hb* > > Marius > > > On Tue, Mar 15, 2011 at 5:40 PM, Maia Cherney <mailto:ch...@ualberta.ca>> wrote: > > > Hi, > > Can anybody a

Re: [PyMOL] hbs

Hi, Can anybody advise me what is the right command for selecting or coloring many hbs? Instead of color black, hb1 color black, hb2 etc I want something like color black, hb1+hb2+hb3 etc. Maia -- Colocation vs. Mana

Re: [PyMOL] delete an hb from a multiple hb object

Hi Jason, I generated hbs from mode=2 method. It made some wrong hbs. How can I delete those wrong hbs? Maia -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organizati

Re: [PyMOL] write a script from pse file

mol. You can save the molecules contained in the session, but the >> graphical representation and any modifications would need to be >> recreated. >> Hopefully Jason proves me wrong ... >> >> Cheers, &g

Re: [PyMOL] write a script from pse file

Hello, I have an old saved session as a pse file. How can I save a script that produced that pse file. It may be easier just to get information about each object in that pse file. Maia -- Colocation vs. Managed Hostin

Re: [PyMOL] Selecting ASP and GLU

For me, color red, resn asp+glu works. Maia Martin Hediger wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within > an object? > > I'm trying it the way its written on the wiki: > remove resn hoh# remove water > h_add # add hydrogens > > a

Re: [PyMOL] map lipophilic potential

Program Vasco can do it. Sebastian Kruggel wrote: > dear all, > > i am looking for a possibility to map lipophilic potential > on pymol generated surfaces. i didn't find anything in the > documentation and in the mailing list the question came up once > > http://www.mail-archive.com/pymol-users@

Re: [PyMOL] pymol dies when minimizing

ion of Windows and PyMOL are you using? > > Cheers, > > -- Jason > > > On Wed, Jun 2, 2010 at 10:52 AM, Maia Cherney wrote: > >> I had once a problem with pymol that itr would not open from a terminal >> window. After a long battle with it, the problem was

Re: [PyMOL] pymol dies when minimizing

I had once a problem with pymol that itr would not open from a terminal window. After a long battle with it, the problem was solved after I upgraded my OS. Robin Emig wrote: > > Does anyone else have the problem where pymol dies, or wont update the > display after minimizing on windows? Is ther

Re: [PyMOL] coordination bonds

Thank you for your help. However, I have 4 Mg ions in the au, so all Mg ions (and all coordinated ligands) got connected. I need only coordination for one Mg. Maia Nathaniel Echols wrote: > On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <mailto:ch...@ualberta.ca>> wrote: > >

Re: [PyMOL] coordination bonds

I found a similar command dist 1, elem mg, elem o, 2.2 Nathaniel Echols wrote: > On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <mailto:ch...@ualberta.ca>> wrote: > > I would like to show coordination bonds between Mg ion and its ligands > (oxygens) as broken lines,

Re: [PyMOL] coordination bonds

I would like to show coordination bonds between Mg ion and its ligands (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A. Maia -- ___ PyMOL-users mai

Re: [PyMOL] Symmetry Mates Problem

In his latest paper E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Krissinel wrote that DGdiss error is 5kcal/mol. I think that DG~5kcal/mol is a gray zone. Then he compares docking results wi

[PyMOL] [Fwd: Re: Symmetry Mates Problem]

Docking is very non-reliable. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Maia humayun scherrif wrote: > Hello, > > Thank you for detailed explanation, surely it is helping me to sort > o

Re: [PyMOL] list of hydrogen bonds

Hi Jason, is it possible to print out a list of hydrogen bonds found by polar contacts. Maia -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: htt

Re: [PyMOL] PyMOL updates

Hi Jason, 1. I am wondering if I have the latest version of pymol. I got it via ubuntu package. How do I update the pymol version? 2. I was trying to do some procedures from the Warren's letter: Builder use: (1) activate the builder by clicking on the "Builder" button on the upper window (2)

Re: [PyMOL] PyMOL Plugin Architecture

Thank, Robert, Jason. Finally I figured this out with your help. Maia Robert Campbell wrote: > Hi Maia, > > Just to add to what Jason said: > > On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees > wrote: > > >>> 2. Which plugin allows me to move one structure relative to another. (I >>> want

Re: [PyMOL] PyMOL Plugin Architecture

Hi Jason, 1. How can I undo a plugin. By mistake I tried to plugin a program using a wrong file and now I get an error message every time I open pymol. 2. Which plugin allows me to move one structure relative to another. (I want to do manual docking of one structure into another). Maia Jason

Re: [PyMOL] pymol and freemol

odules/pymol/__init__.py:freemol_libpy = > os.path.join(os.environ['FREEMOL'],"libpy") > modules/pymol/__init__.py:if os.path.isdir(freemol_libpy): > modules/pymol/__init__.py: if freemol_libpy not in sys.path: > modules/pymol/__init__.

Re: [PyMOL] new ideas

> Regards, > > -- Jason > > > On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote: > >> Hi Jason >> >> I need such features. I open two different pdbs and I want to manually move >> one structure relative to another. I want to dock one structure int

Re: [PyMOL] new ideas

allow you to do small molecule cleanup and editing. > > Try putting your mouse into "Editing Mode" and moving atoms around. > It's not hard. Check this out: > http://pymolwiki.org/index.php/Molecular_Sculpting for some help. > > Regards, > > -- Jason >

Re: [PyMOL] new ideas

Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecu

Re: [PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

Hi John, I have a similar problem with my ubuntu 8.10. When I use a command window, I get the error message: Traceback (most recent call last): File "/var/lib/python-support/python2.5/pymol//__init__.py", line 167, in import pymol File "/var/lib/python-support/python2.5/pymol/__init__.py

Re: [PyMOL] Alignment Objects

Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30

[PyMOL] pymol does not open from a terminal

Hi, Could you please help me with a pymol problem. I have ubuntu linux and I have pymol in the /usr/bin (comes with ubuntu installation) and also one in the /programs/linux directory. But I can't open pymol in a terminal (both installations), only from applications/education menu. I get this er