Dear Pymol Users!
In the latest 3.0 releases of the CAVER plugin lack the source path for the
caver.jar launch file. Could you tell me how I could define this path
manually from pymol shell? I've try to make calculations with thus plugin
having Caver 3.0 dir in the work folder but obtained error
ed.unc.edu/), since the installation and
> compilation can take some time.
>
> Best,
> -Ron
>
> On Nov 10, 2013, at 2:27 PM, James Starlight wrote:
>
> > Dear PyMol users!
> >
> >
> > I'm looking for the possible python script which using the pym
Dear PyMol users!
I'm looking for the possible python script which using the pymol source
would introduce selected mutations in the defined PDB file and produce PDB
output containing such protein with the selected substitution residues. It
would be also good if rotamers for mutation residues woul
Dear PyMol users!
I want to set transparency on the selected carton region of my protein ( I
have closed GFP barell with the chromophore inside it so I'd like set
transparency of some beta-shits to make chromophore easily visible ).
In PyMol I've selected region corresponded to that Beta-sheets
Dear PyMol users!
I have a set of conformations extracted from the MD trajectory (on the
equal time-steps). After loading of all that pdb's into pymol (each
conformer= separate pdb file) I want to sort that structures based on the
RMSD relative to the reference conformer (e.g step0.pdb ) in the s
Thomas,
actually I used very routine way. Firstly I've extract conformers of
protein-ligand complexes from the trajectory. Than I've loaded it into
pymol and visualize possible interactions. Than I've selected most
representative conformers and loaded it separately into pose view to obtain
2D map
Thomas, thanks for help!
As I understood fconv can be used for the split several mol2 (or pdb) files
which was placed in 1 model to the several pdb files, doesnt it ?
In past I forced with some problems with g_hbond. Is there any other way
to monitor h bonds along the trajectory (e.g in vmd) ?
Dear Pymol users!
I want to examine protein-ligand interactions observed in the md trajectory
using Pymol.
For such task I have 100 snapshots of the protein-ligand complex which I've
loaded into the pymol. Now I want to extract from all snapshots 100 ligands
as the separate 100 objects and save
er loading the files:
>
> PyMOL> order *, yes
>
> Cheers,
> Thomas
>
> James Starlight wrote, On 04/02/13 19:28:
> > Pete,
> >
> > thanks for suggestion.
> >
> > I've tried to use loadDir with the pdb's subset where each file had
100.pdb)
> it might be easier rename your pdb files so that the default string sorting
> from glob matches the numerical order you want. Using the same example,
> the filenames would change to 001.pdb, 002.pdb, ... 100.pdb.
>
> Pete
>
> James Starlight wrote:
>
>&g
Dear PyMol users!
I've forced with the problem of the loading of the my structural ensemble
(pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into
pymol via loadDir.pml script. In particular after loading of my ensemble in
the right contex pymol's window I want to preserve struc
at
once ?
James
2013/3/28 James Starlight
> by the way have someone had problems with the pdb2pqr usage with APBS in
> pymol?
>
>
> I've tried to install pdb2pqr from source as well as via packages
> then I've add usr/bin/pdb2pqr to the APBs plugin window
>
arguments!
argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: []
should I provide some addition paths to the bash?
James
2013/3/27 James Starlight :
> As I understood the APBs plugin which already exist in PyMol is the
> very efficient device for electrostatic potential calculations.
&
As I understood the APBs plugin which already exist in PyMol is the
very efficient device for electrostatic potential calculations.
2 questions have been arisen:
1- How I could change cut-off distances for the electrostatic? E.g I'd
like to consider only interactions within 5 A between any charg
Dear PyMol users!
I wounder to know about built-in PyMol option for electrostatic
potential visualisation.
For example I have pdb coordinates of my protein as well as its
electrostatic potential distribution (calculated by another software).
Using MolMol with both of that files I can visualize t
Dear PyMOl users!
I've forced with the problem during installing of the DSSP/STRIDE plugin.
In particular I've download pymol's plugins (and installed it via the
plugin's meny) as well as DSSP binaries.
then I've add DSSP_bin to the bash.rc
so in the terminal I can launch it
own@starlight ~/Do
hmm using TMalign method of superimposition I've solved that problem (
the atom order of ligand have been unchanged).
James
2013/2/7 James Starlight :
> Dear PyMol users!
>
> I've forced with the problem during superimposition of two identical
> proteins. First of all
ng for detailed options of the possible settings in that
file ( e.g I didnt find how to set maximum quality of images as the
default option )
Thanks for help
James
2013/1/26 James Starlight :
> Recently I've tried to find pymolrc but couldn't do it ( I have pymol
> 1.5 installed
Dear PyMol users!
I'd like to build simple 2D lattice model consisted of the Carbon
atoms connected by the single bonds. Could you provide me with some
script which can build such lattices of the desired dimensions ?
Thanks for help
James
--
Dear PyMol users!
I wounder to know about possible way to save settings of the PyMol
after LogOut from it.
E.g I've defined some basic settings like fetch_host and fetch_patch
for uploading of new pdb files as well as set new background colour.
Also I've changed some advanced settings - e.g I de
atom number in the sequence was mixed ( e.g like abababababababab,,
where I need to obtain sequenctial order ).
What I've done wrong and how I could obtain desired sequence ?
James
2012/8/14, James Starlight :
> Dear PyMol users!
>
> I want to create chimeric protei
Dear PyMol users!
I want to create chimeric protein (merge the N term of the second
protein to the C term of the first protein) from two initial pdb's.
How I could do this for further processing of that chimeric protein
for MD simulation ?
Thanks for help,
James
--
Dear PyMol users!
I have pdb structure wich I'd like to prepare for my MD simulation. In
that case this structure consist of some non-standart residue (
chromophore) wich is covalently bonded to the protein's backbone. The
main problem is that this structure has some missing residues on both
of t
Dear PyMol users!
In this topic I'd like to discuss different algorithms of the
structure superimposition included in PyMol. First of all I've already
noticed that some of such algorithms like CE or TMalign (part of the
PSICO) have been already included in PyMol. It's known that such
algoritms mai
Dear PyMol users!
I have big pdb ensembles consisted of 20-100 X-ray structures of
different conformers of common protein solved by X-ray. I want to
obtain single pdb files for such ensembles in NMR-like format.
Firstly I can load all that pdbs into pymol by means of loadDir
script. Now I'd like
Dear all!
I have input multi state structure consisted of protein in one state
and ligand in the second state generated by Chimera. I want to merge
both of that objects in one common object. How I could do it?
James
2012/7/18 James Starlight :
> Dear all!
>
>
> I have input
copy those selected aa's and atoms to another object:
> save -> model -> copied_object as output.pdb
>
> output.pdb will then contain all the x,y,z coordinates of only what was
> selected.
>
> Then just get those columns and upload them to swiss dock.
>
Dear PyMol users!
Some of docking servers (e.g swiss dock) which I'm using need in
explicit definition of the coordinates (in XYZ) of the docking region
as well as coordinates of its COM. How I could obtain such coordinates
of intrested pdb file based on the knowing protein-ligand interaction
sit
Dear Pymol Users!
I've forced with the problem of missing correct atom numbering order during
processing of my pbd structure.
E.g I had a mollecule of caffein where each atoms had its own number ( e.g
N1 or N3 etc)
HETATM 2252 N1 CFF A 330 9.174 -33.156 -31.881
1.00147.73 N
H
ce area. For example:
>
> remove solvent beyond 3.5 of polymer
> set dot_solvent
> get_area solvent, load_b=1
> remove solvent and b > 20
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On 04/26/2012 10:55 AM, James Starlight wrote:
>
>> Another ques
Dear Christian,
thank you for infromation- I'll examine this software. In particular I'm
looking for possible modules for pymol because as I've found previously
it's a good visualisation of the surfaces wich have been already included
in PyMol.
2012/6/28 Christian Roth
>
>
> By the way, there
re or pymol
modules for the analysis of protein-ligand interactions. In particular I'd
like to obtain 3d surfaces of vdw as well as electrosctatics profiles of
the active sites of my proteins as well as analysing of H-bonds ?
James
2012/6/26 James Starlight
> I'm still waiting for a
> Hi James,
>
> hm, looks like PoseView ignores all water molecules :(
>
> Have you tried LigPlot? It has a "-w" option to include waters.
>
> Cheers,
> Thomas
>
>
> On 06/26/2012 05:11 PM, James Starlight wrote:
>
>> Thomas,
>> Its really grea
ow:
>
> http://pymolwiki.org/index.php/PoseView
>
> A LigPlot wrapper may follow...
>
> Cheers,
> Thomas
>
> On 06/26/2012 10:13 AM, James Starlight wrote:
> > Christian,
> > Also I've found the same software- pose view (in that article I've also
&
Christian,
Also I've found the same software- pose view (in that article I've also
found link on it). Its very friendly but I've noticed some erorrs during
representation of the non-covalent contacts partly in case of the vdw
interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some
/1-s2.0-S0005273610001707-g
> > r4.jpg
> >
> > Could you tell me examples of software wich could produce such maps?
> >
> >
> > Thanks
> >
> > James
> >
> > 2012/6/15 James Starlight
> >
> > > Thomas, thanks this works perfe
maps?
Thanks
James
2012/6/15 James Starlight
> Thomas, thanks this works perfect.
>
>
> Jason, I've tested this script on my system ( this is the membrane
> protein inserted in the bilayer surrounded by two water layers ( up and
> down ). During simulation individual wa
Thomas, thanks this works perfect.
Jason, I've tested this script on my system ( this is the membrane
protein inserted in the bilayer surrounded by two water layers ( up and
down ). During simulation individual water mollecules move into the protein
interiour ( in that case protein like a water
. But what exaclty cutt-offs and
addition python modules should I use?
James
2012/4/17 James Starlight
> Thanks, Thomas!
>
> Your script works fine. I've tested in one pdb structure and it finds all
> polar and salt-bridges perfectly.
>
> As I've understood this scr
Oh, it seems that the problem was due to old version 1.3 of PyMol wich has
been installed on my linux work-station. Today I've tried to make the same
mutation on another win PyMol and the result was perfect.
James
2012/6/1 James Starlight
> I've sent another message with attache
On Fri, Jun 1, 2012 at 11:16 AM, James Starlight
> wrote:
>
>> Dear PyMol users!
>>
>>
>> I've tried to make 1 point mutation by means of pymol's mutagenesis
>> wizard and obtain partially broken pdb.
>>
>> In my caseI've changed 27
in my structure there are lack not only side chain atoms
but also two backbone Oxygens in the Gly and Asn wich could be the
main problem of such task.
In any case I'll be very thankfull if you provide me with such server
James
26 апреля 2012 г. 12:55 пользователь James Starlight напис
uot;, chain="A"
>
> See also
> http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter>
>
> Cheers,
> Thomas
>
> James Starlight wrote, On 04/26/12 09:18:
>
> Dear PyMol users!
>>
>>
>> I have some structure.pdb from the md si
ow I could do it?
James
1 апреля 2012 г. 15:04 пользователь James Starlight
написал:
> Thomas,
>
>
> thank you I'll test your script with modeller after obtaining of this
> software on my workstation and post here results :)
>
>
> James
>
> 1 апреля 2012
_raw_distances('**saltbridges', state)
>print ' %2d charged contacts in state %d' % (len(sb), state)
> python end
> --**
>
> [1]
> http://pymolwiki.org/index.**php/Get_raw_distances<http://pymolwiki.org/index.php/Get_raw_distances>
Dear PyMol users!
I'm analysing polar interactions occured during MD simulation of my
protein. In particular I have PDB file obtained from such trajectory where
I'd like to check new polar contacts ( salt bridges first of all) within
selection region. I've tried to select specified region and use
tried
set connect_mode, 1
but saved pdb still have not contained CONNECT :(
Thanks for help
James
30 марта 2012 г. 13:52 пользователь James Starlight
написал:
> Hi all :)
>
>
> Recently I've been needed to parametrise my short protein mollecule by ATB
> server for futher MD simu
Dear PyMol users!
I'm working with the big pdb ensemble wich lack information about the
secondary structure ( deleated header region)
I want to find possible way to assign secondary structure for all pdb's in
my ensemble ( like A-> assign sec.str for specified pdb). Finally I want to
deleate some
is were me though, I would use Biopython.
>
> Jordan
>
>
>
>
> On Jan 28, 2012, at 11:41 PM, James Starlight wrote:
>
>> Dear PyMol Users!
>>
>>
>> I want to make simple chimeric mutant via PyMol by transferring
>> specified group from one prote
Dear PyMol Users!
I want to make simple chimeric mutant via PyMol by transferring
specified group from one protein to another.
E.g I have to proteins:
1 protein consist of triplet of TLG amino acids in the X place
2nd protein consist of specific group wich I w'd like to move in the X
place of
election 1 doesn't contain a single atom/vertex.
I suppose this error might be due to incorect definition of H atom in the
first selection. By the way how I could define PHI in case if my structure
lack for hydrogens at all ?
James
2012/1/27 James Starlight
> Dear Thomas, Jed!
>
>
emb ( like
benzol) because of long distance between adj atoms.
How I could optimise geometry of the new mollecule? Have pymol some
built-in functions like conformational search be means of monte carlo or
energy minimisation ?
James
2012/1/27 Thomas Holder
> On 01/27/2012 09:11 AM, James St
Dear PyMol users!
I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?
James
--
Try before you buy = See our experts in action!
The most comprehensive online learning library for
# activate sculpting
> > sculpt_activate all
> > set sculpting
> >
> > # switch to edit mode
> > edit_mode
> >
> > Now drag atoms with the mouse or pick bonds and use commands like
> "torsion".
> >
> > Hope that helps.
> >
> &g
Dear PyMol users!
I'm looking for the possible way to change some backbone didedral values in
my peptide and dont perturbe the secondary structure of the rest of the
peptide.
E.g I have alpha-helix with sequence x-S-T-G-xI want to make
turn motif in the STG tripeptide only by cha
e to use this for
better prediction of the mutations wich will change the shape and geometry
of the ligand binding pockets in the above cases. \
Thanks again,
James
2012/1/23 James Starlight
> Thanks Thomas
>
> The reversible convertion indeed solved problem.
>
> James
&
:
> http://pymolwiki.org/index.**php/Distance<http://pymolwiki.org/index.php/Distance>
>
> For the potential h-bonds, use it with mode=2.
>
> Cheers,
> Thomas
>
>
> On 01/24/2012 05:15 PM, James Starlight wrote:
>
>> Dear PyMol Users!
>>
>> In t
Dear PyMol Users!
In the PyMol Wizard I've found very userful option called distance
measurements beyween selected atoms.
I wounder to know how I could realize such operation via PyMol console in
the simplest manner.
My current task consist of making different point mutations and subsiquent
qu
Dear PyMol users!
I have one extra question about addition of the missing Hydrogen atoms to
my structure.
I've found that I could do it via context Hydrogen command as well as via
H_add command.
Now I want to add only specific hydrogens to the specific residues of my
proteins ( e.g only alympha
ose that error might be due to the HETATM ussage because when I check
sequence of my structure I'vee found many repeates of the assigned residues
like
THR-THR-THR-THR-TYR-TYR-TYR-TYR-TYR-GLY-GLY-GLY instead of simple
THR-TYR-GLY triplet
What should I do?
2012/1/23 James Starlight
> Tho
Thanks Thomas
I've just one extra question about ligand sites.
As I've said previously I can obtain information about polar contacts
between ligand and its surrounding residues via Present- ligand sites.
On the next step I mask all other non relevant parts of the protein ( wich
are represented a
Dear PyMol users!
I've desided to make this topic for my questions linked with the
mutagenesis wizard setup.
First of all I've already tried to make some point mutations in my proteins
and all worked perfect. I just want ask about definition of the new
torsions for the mutated residue. E.g I hav
Dear PyMol users!
I've decided create new topic about representation of the protein-ligand
interactions via Pymol because of alot of questions wich have been emerged
during last month.
Commonly I use the PyMol built-in command a-> present->ligands sites->
cartoon for the representation of the po
e="4ins" (Your variable)
> propka proteinname (will not work)
> propka 4ins(will work)
> propka.propka(proteinname) (will work)
>
> I hope this clarify a little.
>
> Read more about namespaces here:
> http://www.pymolwiki.org/index.php/Running_Scripts
> http://do
/16 Troels Emtekær Linnet
> It depends on, if you run or import the script. The namespace will be
> different.
>
> What do you do?
>
> This is no error. This is basic Python knowledge.
>
> Troels Emtekær Linnet
> Slotsvej 2
> 4300 Holbæk
> Mobil: +45 60210234
ext, SYG is not in that protein. If you search for "S.G" you find
> SNG. You can double check this by:
>
> fStr = cmd.get_fastastr("1a3h")
>
> print "SYG" in fStr
>
> which return false.
>
> Cheers,
>
> -- Jason
>
>
> On
Dear PyMol Users,
I need to search defined sequence motifs in my structures.
For that purpose I've used
http://www.pymolwiki.org/index.php/FindSeq script
but when I've try to use it I've got error
PyMOL>findSeq SYG, 1a3h
Error: selName was not a string.
There was an error with a parameter. Pl
. I'm getting ready
> for the PyMOL v1.5 release, so you'll get faster answers there.
>
> Cheers,
>
> -- Jason
>
> On Tue, Jan 10, 2012 at 6:22 AM, James Starlight
> wrote:
> > Hi Jason
> >
> > Thank you for help again.
> >
>
> >> > 2011/11/28 Thomas Holder
> >> >>
> >> >> Hi James,
> >> >>
> >> >> most trivial manner:
> >> >>
> >> >> as cartoon
> >> >> show sticks, resn LEU+ILE+VAL
> >> >> set cartoon_side_
er
> >>
> >> and eventually something like this:
> >>
> >> show spheres, resn LEU+ILE+VAL and not name N+O+C
> >> set sphere_transparency, 0.5
> >>
> >>
> >> Cheers,
> >> Thomas
> >>
> >> On 11/28/2011 02:58 PM
omething like this:
>
> show spheres, resn LEU+ILE+VAL and not name N+O+C
> set sphere_transparency, 0.5
>
>
> Cheers,
> Thomas
>
>
> On 11/28/2011 02:58 PM, James Starlight wrote:
>
>> Another question also linked with the non-covalent interaction.
>>
&g
hanks,
James
2011/11/27 Edward A. Berry
> Yes i think the strongest H-bonds are single acceptor and straight
> (angle at H = 180*). but these other bonds have significant
> strength also.
> Sorry, I'm a complete beginner at pymol. I have no idea how to
> do these things.
>
Thomas, thank you for so detailed explanation.
This way works good but I'd like to ask you about possibe Hbonds in the
protein chain.
As I remember for protein physics courses the H atom is always donor for
only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds)
But In my case t
he bottom right of the viewer.
>
> ** **
>
> Joel****
>
> ** **
>
> *From:* James Starlight [mailto:jmsstarli...@gmail.com]
> *Sent:* Thursday, 17 November 2011 7:52 a.m.
>
> *To:* Joel Tyndall
> *Subject:* Re: [PyMOL] Editing of the pdb structure
Dear PyMol users!
As I've understood there are no posible ways to represent H-bonds in
proteins in explicit manner. So I'm looking for possible way to do it via
some plugin or another way.
In particular I need
1) to visualize H-bonds in some structural motifs like coiled coil wich are
dimers of
Dear PyMol Users!
I've decided to make this topic for all questions wich could be arrise
during working in diffent PyMol plugins.
So My first question about installation of the plugins wich are separate
python modules ( installed not via PyMolf itself)
E.g I have old PyMol wicj lack CEalign plug
ow i could specify exactly location of that attachment if i want that
ACE just be the first residue in my pdb ( linked with the actual first
residue on the N term )?
James
2011/11/23 James Starlight
> Thanks Thomas!
>
>
> Those scripts works fine. Could you tell me if there any w
Thanks Thomas!
Those scripts works fine. Could you tell me if there any way to install all
of those scripts as the pymol plugins ( that I need not to load this
scripts every time when I sttart pymol de novo )?
James
2011/11/23 James Starlight
> Thanks thomas
>
> Those scripts w
Dear PyMol Users!
I wounder to know about possible ways of creation of the peptide structures
via PyMol Builder module. In particular I need create a linear structure of
my protein ( with fixed phi and psi angles) for futher folding molecular
dynamics simulation of that peptide. But in builder mod
l but for just one
reference ( similar to the align ) so I'd like to obtain multiple sequence
alignment on one reference based on the multiple structure alignment.
Thanks
James
2011/11/21 James Starlight
> Jason,
>
> but as I've understood super did alignment only for two struct
Jason,
but as I've understood super did alignment only for two structures, Is
there any way to do the same operation for ensemble ? (for CE as I
understood this could be done by alignto command but it lack for seq
alignment iin this case)
James
2011/11/21 Jason Vertrees
> Hi James,
>
> > set
gt; http://pymolwiki.org/index.**php/DynoPlot<http://pymolwiki.org/index.php/DynoPlot>to
> enable postscript export (was quite easy).
>
> Cheers,
> Thomas
>
>
> On 11/18/2011 10:31 AM, James Starlight wrote:
>
>> Thomas, hello!
>>
>> In the past I'v
Thanks, Thomas
It works fine!
Could you tell me in what strings the marker for the particular ss element
is defined ( e.g I want to change from triangle to oval representation for
alpha-helixes )?
Thanks Rober I'll try investigate both of that programs,
James
2011/11/17 Robert Immormino
> Ja
php/Set_Dihedral<http://pymolwiki.org/index.php/Set_Dihedral>
> http://pymolwiki.org/index.**php/Torsion<http://pymolwiki.org/index.php/Torsion>
>
> And you can modify torsion angles interactively using the mouse while in
> editing mode (pick one atom, then CTRL-Drag).
>
>
Dear PyMol Users!
I wounder to know about posible ways to plot for my structures different
torsion angles (phy, psi, chi ) on the ramachandran map via pymol.
In particular I would like to obtain the next information
1- I d like to visualise and measure different torsions for my structure
and pl
Dear Pymol Users!
I want to solve one methodologycal problem via Pymol. I have 20 x-ray
structures of one protein presented in different conformations.
The main problem is that all those structures consist of Hen Lysozyme
inserted in the protein for the improvement of the crystallographic
proper
Dear PyMol users!
I want to prepare my pdb structure for MD simulation with gromacs
1- I want to place some CAP groups like ACE or NH2 to N and C termii of 1
and last residue of my protein, respectyally.
I found possible option for this in the build- amono acids
buit creted via this way ACE or N
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