[PyMOL] calculate angle protein-membrane

Hi all, is there any way to calculate the angle between the axis-protein and a surface membrane? thanks regards, andrea

[PyMOL] script feedback: how print out distance and not average

Hi all, this script below runs well in pymol. It loads pdb files and calculates the distance of some atoms contained in the fileAmb whose format is: 26,O11:HN 28,*:HE1 ... With * I select whole ligand (segi B) and pymol returns only one value, the average distance for all atoms to the H

[PyMOL] feed value to pymol -qrc script.py

Hi there, I made a script in pymol and I'd like to use it as pymol -qrc script.py argv[1] argv[2] ... but it seems not working properly. It says that it cannot open such file, even if the argument is a number... In fact, if I replace the sys.argv[] with the values into script.py, it woks. Any

[PyMOL] very slow script for distance calculation

Hi all, is it normal that a script in pymol runs very very slow. In my case I am just selecting a residue of a protein and calculating the distance from the ligand atoms. I am doing this in a loop over 100 molecule. It took ca. 6 hours...! My memory is 50% free (1Gb total). I am using this scri

Re: [PyMOL] very slow script for distance calculation

Jules Jacobsen wrote: Hi Andrea, It depends on how you've written it It does sound more than a little slow if you are just selecting a single residue. I had a script which ended up looping through several sets of atoms which took ages for larger models. I finally got fed-up with this and

Re: [PyMOL] very slow script for distance calculation

Hi again, reading my post I found the bottleneckshame on me :) here it is: ... if (atomlig == "*"): ligand = cmd.select("ligand","segi B and "+i) atoms_lig = cmd.get_model('ligand') for atomsL in atoms_lig.atom: t = cmd.select("t","name "+at

Re: [PyMOL] very slow script for distance calculation

Gilleain Torrance wrote: Hi, I don't see how you can get rid of this loop actually. The thing that occurs to me is that you are loading structures, but not deleting them! So, at the other end of the "for i in KeepStruc" loop, you should have a "cmd.delete(i)". Other than that, you don'

Re: [PyMOL] Viewing cavities?

what about Caver: http://loschmidt.chemi.muni.cz/caver/concept.php very nice and it works very well andrea 2005/11/7, Bingding Huang : > > Dear all, > > I download CASTpyMOL.pyc and put it in the right folder. > Now I want to use it for detecting cavity for 50 proteins. I don't want > to do tha

[PyMOL] combine align and rms_cur to calculate rms for complexes

Hi all, could someone confirm this: I have some complexes protein+ligand and I'd like to perform rms calculation for the position of the ligand. This what I have done: load reference.pdb select proteinreference, segi A select ligreference, segi B load compare.pdb select proteincomapre, segi A sele

Re: [PyMOL] combine align and rms_cur to calculate rms for complexes

Hi Warren, yes this is the case. My complexes are from a docking calculations with the same ligand. I was just quite doubtful about the procedure... to use align and then rms_cur. I compared the rms results with another software (vmd) and it seems to be consistents. Thanks, Regards, andrea

Re: [PyMOL] display of multiple NMR structures stored in one PDB file

Hi,you can either with mouse clicking on the left-down on ">" or on the menu display all frames. I hope this can help, Regards andrea 2006/1/13, Michael Weber : > > Hello, > I have a short question concerning the display of multiple NMR structures > stored in one PDB file. When loading NMR .PDB

Re: [PyMOL] Surface of cavity

Hi, you may try to use caver: http://viper.chemi.muni.cz/caver/concept.php or castp http://cast.engr.uic.edu/cast/oldindex.php regards andrea 2006/1/21, Paul Wilhelm Elsinghorst : > Hi, > > > a little question regarding cavity surfaces :-) > > > I have a set of active atoms (GOLD output) t

Re: [PyMOL] (no subject)

Hi try align or fit regards andrea 2006/3/3, srilath...@jubilantbiosys.com : > dear all > can we superimpose structures in pymol > Thanks & Regards > srilatha potlapelly > MSc Biotechnology > Drug discovery, > #450,4th D Main, 12th cross, > Mahalakshmipuram - 560086 > Bangalore > Office: +9180-2

[PyMOL] pymol-099rc6 installation problem on am64bit

Hi all, I have downloaded pymol-099rc6 and followed the instructions to install it. Typing pymol I get back: pymol.exe not such file or dir even if the pymol exec is there. My laptop is an amd64bit hp pavillon thanks andrea -- "La conoscenza libera il genere umano dalla superstizione" J. Wa

Re: [PyMOL] (no subject)

Hi, for this purpose I have used caver program. You can download it free of charge from here http://loschmidt.chemi.muni.cz/caver/download.php I hope this help Regards andrea 2006/3/27, srilath...@jubilantbiosys.com : > dear sir > iam a pymol user, do we can find area & volume of a

Re: [PyMOL] surfaces

Hi I think you should select the chain A and then create the object for this selection. Then you can manipulate as standalone object. select A, chain A create A_obj, A show A_obj,surface I hope this help Regards andrea 2006/3/28, Chandra : > If I have two chains in a structure how can i draw a s

[PyMOL] load *only one* state for NMR ensemble ..

Hi all, I have more then 200 pdb files and each file represents an ensemble of NMR calculated structure (ca. 30). If I try to load all together, my system goes terribly slowly and pymols seems crashing (the windows freeze). Is there any way to load only the first structure for each file rather than

Re: [PyMOL] pymol on amd64?

Hi, few weeks ago I had a problem with pymol-32bit on my laptop 64bit using slamd Warren built a pymol for 64bit and you can download it from here: http://delsci.com/beta/ In my case it worked. Regards andrea 2006/4/11, Florian Haberl : > hi, > > On Tuesday 11 April 2006 19:59, Praedor Atrebat

Re: [PyMOL] pymol on amd64?

difference between the Mandriva 2006 > system and SuSE that apparently allows a 64 bit build to proceed. > > praedor > > On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote: > > Hi, > > few weeks ago I had a problem with pymol-32bit on my laptop 64bit using &

[PyMOL] align and iterate residues

Hi all, I found very nice the align command in order to align domains within huge complex. However, I was wondering whether is it possible to iterate on the superimposed structure in order to know "which with wich" residues. Creating the object, I cannot iterate on it. Thanks for any suggestion Re

[PyMOL] align states

Hi all, in pymol is it possible to align states rather than object. I mean, I have loaded a pdb file with n-structures and I'd like to align each of them on the first one of the bundle. Thanks in advance Regards andrea -- Why stand on a silent platform? Fight the war, fuck the norm (RATM)

Re: [PyMOL] align states

t; split_states my_struct > dele my_struct > > > for the NMR ensemble, then I would use the action menu, align function > and align them to state_1. This is in effect aligning the separate > states as objects, unless I misunderstood you > > J > > Andrea Spitaleri wrote:

Re: [PyMOL] Show residues and sticks

1) I superimposed two protein structures. They are similar but have different numbering of residues, e.g residue 34 in structure A is equivalent to residue 38 in structure B. I want to show only the side chain of residue 34 for structure A and residue 38 for structure B. I selected only structure

Re: [PyMOL] apbs plugin in pymol

Hi, at this purpose, what kind of range (positive - negative) should be used in order to visualize correctly the potential surface on a protein? Normally I used -10 to +10 but I am wondering how you behaves with this issue too. Thanks in advance andrea 2006/11/23, D. Eric Dollins : Florian, I

Re: [PyMOL] colour by rms...

Hi, you may try to change the B-factor with the rmsd values normalised from 0 to 100 let' say .. and then colour by spectrum->b-factor. Probably there is another better way ... i dunno :P Regards, andrea 2007/4/4, David Briggs : Hi everyone... I'm sure this has been covered in the pymol maili

Re: [PyMOL] How to see all models in PDB file?

Hi, try movie -> show all states and 2007/6/6, Kristoffer Torbjørn Bæk : Hi everyone, I have a PDB file containing the coordinates for six monomers together forming a hexamer. Each monomer is separated by MODEL/ENDMDL in the PDB file, but when I load the file in PyMOL I only see one of the mo

[PyMOL] overlay ligands inside of protein

Hi everyone, I am quite new here (I have been reading your post in past...) and now I decide to post a question (easy maybe). I couldn't find any answer on Google. I have got two complexes of (protein+ligand)1 and (protein+ligand)2 where the only difference between the two is the different orientat

[PyMOL] new ext file

Hi, sometimes I enjoy coding in Python and Perl. I am having fun to add to Perlmol a module for reading a my own extension file (*.nmr) I would like to do the same with Python. Is there any tutorial where it is explained how to add a new extension file in pymol? I mean, how to make a script for rea

Re: [PyMOL] orient the molecule

Hi, I think that you should use translate[x,y,z] to change the coordinates of your molecule bye andrea 2005/4/21, Bingding Huang : > Hi, > When I try "orient" command to orient the molecule, the camera changes > but the coodinates don't change. > I wonder whether it is possible that when I orie

[PyMOL] import pymol

Hi guys/girls easy and quick question: how can i import pymol modules in my python scripts? ie. I want use translate... do i need to import what? thanks a lot andrea

[PyMOL] still unresolved import pymol...

After any answer, I have been looking on this list and googling around (sorry if I didn't before...) there is: # set path in order to use pymol modules export PYMOL_PATH=/usr/local/pymol/ export PYTHONPATH=/usr/local/pymol/modules/ then type python to enter in the shell and: s...@darkstar:~> pytho

[PyMOL] fit command

Hi all, i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb contains the protein A and docked.pdb the protein A + a docked ligand. when I try to run fit ref, docked I get: ExecutiveRMS-Error: No atoms selected. I tried to select the atoms or create a new object but i get the same result

Re: [PyMOL] fit command

Thanks, it worked. So why fit did fail in doing that? Regards andre 2005/6/20, Ramesh Sistla : > Andrea Spitaleri wrote: > > Hi all, > > i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb > > contains the protein A and docked.pdb the protein A + a docked liga

[PyMOL] Renumber protein segid

Hi all, I couldn't find any command in pymol to renumber the segid of a protein. Is there any way to do it? Regards andrea

Re: [PyMOL] Renumber protein segid

ipts/pdb-mode.html > > Cheers > > Joel > > Andrea Spitaleri wrote: > > >Hi all, > >I couldn't find any command in pymol to renumber the segid of a protein. > >Is there any way to do it? > > > >Regards > > > >andrea > > &g

[PyMOL] run script

Hi this is my "unsuccessful" first script for pymol. I have a series of files: prot1.pdb prot4.pdb prot55.pdb and so on I'd like to open them using a loop (instead to open one by one) I cat them to a file and then I tried to open all of them in pymol: from pymol import cmd file=open("file.nam") fo

Re: [PyMOL] run script

Hi, yes it worked. that mistake is so shameful ... :P thanks andrea 2005/6/30, lie...@ultr.vub.ac.be : > On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > > from pymol import cmd > > file=open("file.nam") > > for i in file.readlines(): > > cmd.l

[PyMOL] apbs

Hi I have been using apbs and the built-in generate electrostatic surface. I'd like to know your impression on which tools is the best for MEP calculation. thanks a lot Regards andrea

Re: [PyMOL] loading multiple structures from one file

Hi try Movie -> select all state it should work andrea

[PyMOL] script to write down distances ligand-protein: need feedback

Hi guys, I am trying to make a script to automatize a procedure. I have got a file where I can pick up the structure of protein-ligand complexes cluster The script below read the number of the cluster and then visualize them align with a protein reference. Everything is fine except I'd like write o

Re: [PyMOL] script to write down distances ligand-protein: need feedback

> HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) yes thanks for the trick. However, I edited my script to: DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd")) DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD)) but I cannot figure out the mea

Re: [PyMOL] rearranging the coordinates of a PDB file

Hi Vanessa, try also pdb-mode.el (http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html) I have been using it for a while and I found very useful Regards, andrea

Re: [PyMOL] script to write down distances ligand-protein: need feedback

ways going to be computationally > expensive, but I don't know ways to speed this up. > > gilleain torrance > > > On 5/7/05 15:17, "Andrea Spitaleri" wrote: > > >> HBA = cmd.distance('HBA', '(lig and acc)','(active and don

Re: [PyMOL] Plotting electrostatic surfaces

Hi you should install the apbs plugin and read the input file http://www-personal.umich.edu/~mlerner/PyMOL/ cheers andrea 2005/7/7, Akanksha Nagpal : > Dear PyMol Users: > > I have a .pqr file and am wondering if I can use this file in Pymol to draw > electrostatic surfaces in a ligand bindi

[PyMOL] select all aminoacids and not ligand

Hi all is there any shortcut to select all aminoacid in a complex and not the ligand? something like select my, all and not "ligand" where I don't know the resn of the ligand but in my script I should be able to discern between aminoacids (ALA,VAL, etc...) and not. thanks in advance Regards andre

Re: [PyMOL] select all aminoacids and not ligand

Hi, thanks. that was my first answer and it works. but in case the chain id are the same? and 2005/7/12, Marc Bruning : > in case your ligand has a different chain id than your protein, you could use > that to distinguish. > > On Tuesday 12 July 2005 11:59, Andrea Spitaleri wrote

[PyMOL] select ligand in just one complex

Hi all, I know it seems trivial but it doesn't work. load different complexes and I want select a ligand just in one structure: select my_lig, resn CBO in complex1 but it select CBO in all complexes . what is it wrong? and

Re: [PyMOL] antialiasing and povray

try povray +A0.3 file.pov zero -^ regards Cameron Mura wrote: hi, Is there anything special I need to do/set to achieve antialiased images via pymol + POV-ray? To be more explicit, i'm using robert campbell's make_pov.py to have pymol dump the scene into a povray input file, and

[PyMOL] [OT] alternative python module

Hi all, I am using pymol also for python scripting and perlmol for perl scripting. They are both very nice. I am just wondering if there are some other useful python modules around for chemistry. Sorry for the OT. Regards, andrea

Re: [PyMOL] [OT] alternative python module

://frowns.sourceforge.net/) MMTK (http://starship.python.net/crew/hinsen/MMTK/) All these software are free software. Regards, Jerome PANSANEL -- Jerome PANSANEL http://www.alchem.org Le Lundi 25 Juillet 2005 15:42, andrea spitaleri a écrit : Hi all, I am using pymol also for python scripting