Re: [PyMOL] Fetching scripts

olution. > http://p.sf.net/sfu/whatsupgold-sd > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users

Re: [PyMOL] Editing of the pdb structure

- > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learnd

Re: [PyMOL] list of polar contacts

listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ====== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athe

Re: [PyMOL] list of polar contacts

ed in the window. > It should be possible I guess. > > Do you have more ideas? > > > > > On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis wrote: > >> Probably because they set diffently the acceptor-donor cutoff and the >> acceptor-hydrogen-donor angle. Use

Re: [PyMOL] Editing of the pdb structure

protein with the some non-standart functional group like GFP > > So the servers like PRORG are not good for that because of big size of the > protein and subsiquent integration of both fragments. > > James > > > 2012/1/30 Thomas Evangelidis > >> Is it a small organic m

Re: [PyMOL] Visualization of the protein-ligand interactions

oms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemi

[PyMOL] Fwd: Visualization of the protein-ligand interactions

ly monitor H-bonds with g_hbond from GROMACS Tools and >> Salt-Bridges with the respective VMD plugin. Then I make a table with >> frequences of each polar interaction, pick up a frame that contains as many >> important interactions as possible, load it in PyMOL and draw dotted lines &

Re: [PyMOL] SS in a trajectory

sts/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Che

[PyMOL] arranging atom records in pdb file by resid

r any other program please let me know. thanks, Thomas -- ====== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email

[PyMOL] how to visualize the results form flexible sidechain ligand docking

)? thanks, ~Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr

[PyMOL] forward and backward keyboard shortcuts

Hi, Is there any keyboard shortcut to move to the next or the previous state of an object, namely something equivalent to "forward" and "backward" commands? -- ====== Thomas Evangelidis PhD student Universi

[PyMOL] command to deactivate/hide an object

(hide it) then I could visualize the structures one by one once they are all loaded -which is actually what I want. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of

Re: [PyMOL] Making nmr-like ensemble from several pdbs

-- > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinf

Re: [PyMOL] Making nmr-like ensemble from several pdbs

el to use*. > > But still it says you can use only one at a time. > i guess it indicate that in principle some ensembles are possible as the > input :) Alternatively do you know any other tools (software) for the > processing of the ensembles with such options for the analysis?

[PyMOL] polar contacts involving F, Cl and S atoms

Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S atoms. There's a tutorial on the wiki that explains how to set the cutoff distance but that refers only to O and N atoms: http://www.py

Re: [PyMOL] polar contacts involving F, Cl and S atoms

no one has a better guess, maybe try 1.7 plus the VDW radii of F (1.35), Cl (1.8), or S (1.85). Seems like a good guess to me. Cheers, -bob On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis wrote: Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, b

Re: [PyMOL] polar contacts involving F, Cl and S atoms

ss to me. Cheers, -bob On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis wrote: Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S atoms. There's a tutorial on the wiki that expl

[PyMOL] where to find a 64 bit Linux version?

Dear Pymol users, does anyone know where I can find a 64 bit version for my Fedora 10. The package from the repositories works fine but when it comes to install new plugins it yields error messages. As a matter of fact I can't even figure out where the whole program is installed (used loc

Re: [PyMOL] where to find a 64 bit Linux version?

ion...silly me! On Wed, 18 Mar 2009 01:03:07 +0200 Thomas Evangelidis wrote: Dear Pymol users, does anyone know where I can find a 64 bit version for my Fedora 10. The package from the repositories works fine but when it comes to install new plugins it yields error messages. As a matter of f

[PyMOL] how to get RMSD from align command

Simple question, it must have been answered before but couldn't find it so far: how can I get the RMSD value from the align command in a python script? cmd.align() returnes a tuple of 8 numbers and none of them is the actual RMSD value I get when I align these 2 structures manually. thanks,

Re: [PyMOL] how to get RMSD from CEalign command

PI calls. > > align > is nearly equal to > cmd.align(quiet=0) > > Thus, if you want to get rmsd output, include quiet=0 and run your > script with output redirection. > > > Andreas > > > > On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis > wrote: >

Re: [PyMOL] how to get RMSD from align command

of aligned atoms is the second > field. > > If you're looking for exact RMS fit values over a well-defined set > of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example: > > load $TUT/1hpv.pdb > > create loopA, A/46-55/ > > create loopB, B/46-55/

Re: [PyMOL] how to get RMSD from align command

In other words, you can > compare any number of C-alpha positions so long as the same number > of atomic positions are specified in each structure. > > Cheers, > Warren > > -Original Message- > From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] > Se

Re: [PyMOL] how to get RMSD from CEalign command

> Thomas, > > The PyMOL UI runs asynchronously. I think you are deleting your PDB > files before they can be aligned. I made a couple changes in your > script. Instead of calling cmd.do just call cealign directly. See > below, > > query_template_chains = { > "1ebh" : ["1ebg", "1els", "1one", "2on

Re: [PyMOL] how to get RMSD from CEalign command

command in your namespace after the cmd.do. Have you tried running > > cmd.do("your/path/to/cealign") > cealign(protA, protB)? > > I just tried this on my system and it worked for me. Let me know if it > works for you. > > -- J > > Jason Vertrees, PhD > &

[PyMOL] asymmetric transformation matrices

Dear pymol users, I noticed something strange when superimposing 2 opposite pairs of chains. E.g. DEBUG: template 1BQG_A query 2MUC_A Query Transformation: X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + -0.04181*(Z1+64.71239) Y2 = -0.49701*(X1+2.29751) + -0.85983*

Re: [PyMOL] asymmetric transformation matrices

entical residues in 1ONE x 2ONE and this in 2ONE x 1ONE: ", RMSD check_for_symmetry("1ONE", "2ONE") PS: Jason, I suspect the same happens with CEalign although I couldn't manage to run it for technical reasons, but by looking at the transformation matrices pr

Re: [PyMOL] asymmetric transformation matrices

As Tsjerk pointed out, there was a mistake in the code. Just for the record this is the right function: pdb2entry = { "1ONE": "1ONE_A", "2ONE": "2ONE_A" } # a function to measure Ca distances of oposite pairs of superimpossed chains (the proteins must have the same aa composition) def check_fo

[PyMOL] RMSD produced by align command

Dear pymol users, I'm trying to understand how align command measures the RMSD between 2 homologues and explain the discrepancy between that value and the one obtained from ProFit. The sequence alignments produced by both programs are continuous and match, but the RMS values are 1.781 and

Re: [PyMOL] RMSD produced by align command

ign, intra_fit_rms. > > Hope this helps, > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Tue, Dec 29, 2009 at 1:27 PM, Thomas Evangelidis > wrote: >> Dear pymol users, >> >> I'm trying t

[PyMOL] negative image of binding cavity

Dear Pymol users, I want to display clearly the volume of a buried cavity inside my protein. Does anybody know how to do this? I've tried CastP and Caver plugins already, but they do not produce exactly the volume I want to display. I would greatly appreciate any advice. thanks, Tom -

[PyMOL] How to catch PyMOL command exception within a Python script

ssible to catch this exception from within the script using "try: ... except :" statement? Thanks in advance. Thomas -- == Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/str

Re: [PyMOL] How to catch PyMOL command exception within a Python script

for i in id1], mode='index') > cmd.select_list('sel2', obj2, [int(i) for i in id2], mode='index') > cmd.pair_fit("sel1 and aln", "sel2 and aln") > cmd.delete('sel1') > cmd.delete('sel2') > > Ho

Re: [PyMOL] How to catch PyMOL command exception within a Python script

always create a > named selection first to check if it's valid. > > tmpsele1 = cmd.get_unused_name('_sele1') > try: > cmd.select(tmpsele1, someexpression, 0) > except pymol.CmdException: > print('invalid selection') > finally: > cmd.dele

[PyMOL] cannot write text commands after pymol-open-source installation

xt and previous molecules in a multi-mol file. Does anyone encounter a similar problem? Any idea how to fix this? Thanks in advance. Thomas -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemist

Re: [PyMOL] Script for drawing docked ligand-active site pics

at: https://github.com/tevang/tutorials/tree/master/show_ligand_interactions -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <ht

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

Best regards, > > > > Blaine > > > > Blaine Mooers, Ph.D. > > Associate Professor > > Department of Biochemistry and Molecular Biology > > College of Medicine > > University of Oklahoma Health Sciences Center > > S.L. Young Biomedical R

Re: [PyMOL] New MD/Structure analysis script

om/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Bioche