Hi
both of them are present in my ensemble. the problem is not here- if it
possible i could upload the ensemble.pdb to some server if someone could
check it.
James
2014-08-27 14:52 GMT+02:00 Justin Lecher :
> On 27/08/14 07:43, James Starlight wrote:
> > and than how to quick merge
is it working here?
https://www.sendspace.com/file/8i0aqo
James
2014-08-27 14:58 GMT+02:00 Justin Lecher :
> On 27/08/14 07:56, James Starlight wrote:
> > Hi
> >
> > both of them are present in my ensemble. the problem is not here- if it
> > possible i could uplo
Alternatively do you know any other tools (software) for the
processing of the ensembles with such options for the analysis?
James
2014-08-27 15:05 GMT+02:00 Thomas Evangelidis :
>
>
>
> On 27 August 2014 15:43, James Starlight wrote:
>
>> and than how to quick
Dear PyMol users!
I'd like to find possibilities for running of some pymol commands from the
terminal. For instance in my case I' d like perform 2 simple steps (both in
terminal not in the pymol GUI)
to remove water and ions from my target input pdb (typical I do it via
gromacs editconf)
superimpo
> grep -v "^ATOM.*SOL" in.pdb > out.pdb
>
> To remove NA+/CL- too
>
> grep -v "ATOM.*\(SOL\|NA+\|CL-\)" in.pdb > out.pdb
>
> The fitting is a bit more cumbersome :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Sep 4, 2014 at 10:19 AM
ed to do part of this using
pymol ref.pdb tarr.pdb -cd "super tarr ref"
but eventually obtained error
James
2014-09-04 15:47 GMT+02:00 James Starlight :
> Thanks Guys!
> I'll check the tutorials.
>
> All the best,
>
> James
>
>
> 2014-09-04 13:15 GMT+02:0
nkful for any useful grep awk sed tutorial in case of
the bioinformatics application
James
2014-09-04 16:03 GMT+02:00 James Starlight :
> one question :)
>
> could someone explain me the ussage the pymol commands from the shell on
> the example
> e.g i need to load 2 pdbs in pymol
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:54 GMT+02:00 James Starlight :
> thanks!
>
> and d
1]
> tarfile = sys.argv[2]
> outfile = sys.argv[3]
>
> cmd.load(reffile, 'ref')
> cmd.load(tarfile, 'tar')
> cmd.align('ref', 'tar')
> cmd.save(outfile, 'ref')
>
>
> Then on the command line call it like: python my_align.py reffile
should to add
than I've used both TMalign and mammoth utilities but didn't understand how
to obtain superimposed output as the full-atomic pdb's. I will be thankful
if someone could share with me its experience :)
James
2014-09-05 12:00 GMT+02:00 James Starlight :
> Thanks M
;
> I have a light version for fitting gromacs' gro files. No time to adapt
> that now for PDB, but it's not too hard.
>
> ./qfit.py source.gro target.gro > output.gro
>
> Hope it helps,
>
> Tsjerk
>
>
> On Fri, Sep 5, 2014 at 12:31 PM, James Starlight
&
ish_launching()
AttributeError: 'module' object has no attribute 'finish_launching'
it seems that pymol could not been imported (in my case it has been
installed by package manager and normally called from the command line)- so
to avoid such problems I have not to use python
Dear Pymol users!
I've decided to open new topic focused on the implementation of the common
shell utilities like grep awk and sed for the structural bioinformatics
tasks like processing and editing of the large sets of pdbs.
In my current task I need to copy all lipids from one pdb (called it re
; I have used ProFit for that task, from Andrew Martin's group at UCL. It
> does least-squares fitting, so it's reasonably quick.
> http://www.bioinf.org.uk/software/profit/index.html
>
> Jed
>
> On 9/5/2014 6:00 AM, James Starlight wrote:
>
>> Thanks Matthew,
&
Thomas,thanks for help- I'll try to test your script!
Jed, many thanks too!
if I understood correctly align.profit should contain thefollowing lines:
# using ProFIT to align the model to 2hi4
open $PROFIT, "> align.profit" or die "Cannot open file align.profit\n";
print $PROFIT "ATOMS CA
e contents
>
> Venlig hilsen
> Folmer Fredslund
> Den 05/09/2014 19.16 skrev "Gianluca Santoni" :
>
> Don't even need cat
>> simply do
>>
>> grep PPC ref.pdb > tar_i.pdb
>>
>> redirecting std out with > appends it directly to
uot;;
> >
> >
> > James
> >
> >
> >
> --
> > Slashdot TV.
> > Video for Nerds. Stuff that matters.
> > http://tv.slashdot.org/
> > ___
re ensemble
>
>
>
> Hope that helps!
>
>
>
> Markus
>
>
>
> *From:* James Starlight [mailto:jmsstarli...@gmail.com]
> *Sent:* Monday, September 08, 2014 6:52 AM
> *To:* pymol-users
> *Subject:* Re: [PyMOL] Access to pymol commands from the terminal
>
&g
;ll thankful to everyone who have faced with the same problem and
could provide me with some suggestions.
Thank for help,
James
2014-09-09 12:35 GMT+04:00 James Starlight :
> Thanks Markus, I'll try to examine it!
>
> Jed,
>
> the main problem with the profit is that I need
db > model1.pdb
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight :
> Thanks you very much!
>
> James
>
> 2014-09-05 20:18 GMT+02:00 Folmer Fredslund :
>
>> Hi
>>
>> Small correction to Gianlucas suggestion
>>
>> ">
s,
>
> These are the sort of questions that'll be answered elsewhere. Most
> notably on stackoverflow:
> http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
>
> csplit -b "%04d.pdb" file.pdb /^MODEL/ {*}
>
> Cheers,
>
lines except that
> ones in the expression. Without that you _only_ "grep" the lines with
> those expressions.
> (egrep might be grep, or something similar depending on OS or variant of
> it)
>
> And sed (stream editor) then s(ubstitutes) ENDMDL with TER.
>
> h
Thank you very much!
James
2014-09-12 12:36 GMT+02:00 Marko Hyvonen :
> On 12/09/2014 11:26, James Starlight wrote:
>
>> grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK"|
>>
>
> I think you are missing few "|" in there:
>
> grep -v &quo
'^xz' log.txt | awk '{print ($2, $3 )}' > 2_3columns_from_the_xz.dat
James
2014-09-12 12:51 GMT+02:00 James Starlight :
> Thank you very much!
>
> James
>
> 2014-09-12 12:36 GMT+02:00 Marko Hyvonen :
>
>> On 12/09/2014 11:26, James Starlight wrote:
>
rks perfect
ProFit>FIT
Fitting structures...
RMS: 7.134
Where I made error?
James
2014-09-12 9:13 GMT+02:00 James Starlight :
> Hi Jared,
>
> yes from pymol it's OK, here I've mentioned about ProFit :) but this also
> have been solved. ;)
>
> James
>
> 2
Dear Pymol users,
I've decide to make a copy of this topic from the amber mail list because
this problem could be solves by ones of the methods implemented in Pymol.
Here I'm facing with the problem of the preparation of protein-ligand
complexes for amber md simulation:
Following amber's tutorial
.0/) or through the APBSTools GUI in
> PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can
> use AMBER parameters both for proteins and for ligands (mol2 format). Your
> result would be the structure of your complex, with hydrogens, in the AMBER
> format.
>
>
tial model are not a big
> deal, in my opinion.
>
> Cheers,
> Gian
>
> On 9/17/14 3:17 PM, James Starlight wrote:
> > Hi Fotis,
> >
> > thank you very much for the suggestion!
> >
> > Indeed I have not had such problem with the preparation structure
pype/
>
> This should work fine later to start your md simulations as it should
> conserve your docked coordinates.
>
> Cheers,
> Gian
>
>
> On 9/17/14 3:56 PM, James Starlight wrote:
>
>> all manual and GUI operations are not accepted here!
>> I'm deal
ny other alternatives which could be used as parts of
the shell script.
James
2014-09-15 18:52 GMT+04:00 James Starlight :
> Hey,
>
> I've occasionally deleted my profit script which do superimposition
> automatically so I'll be very thankful if someone remind me profit input
&
Dear Pymol users!
It's probably that my next question will be slightly uncommon but presently
strongly looking for new (post-doc level) position I'd like to obtain some
advises from the expirienced persons like the auditory of this community.
This time having PhD in theoretical biophysics I wound
pe it helps,
>
> Tsjerk
>
> On Fri, Sep 19, 2014 at 10:09 PM, James Starlight
> wrote:
>
>> Dear Pymol users!
>>
>>
>> It's probably that my next question will be slightly uncommon but
>> presently strongly looking for new (post-doc level) positio
graphic pattern ?
James
2014-09-20 10:48 GMT+04:00 James Starlight :
> Hi Tsjerk ,
>
>
>
>
> *Thank you very much for the information!I've already familiar with some
> Adam's works from the textbooks which were really impressed me! BTW do you
> know any advan
Dear Pymol users!
In this topic I've decide to put all questions regarding visualisation.
This time I'm very intresting whether it possible to add some effect of the
"flexebility" or "ensemble-like dynamics" on the selected elements (e.g
selected side-chains to convey a sense of its flexibility
h mobile on it (like fitting in case
of super) ?
James
2014-09-22 10:21 GMT+02:00 James Starlight :
> Hi Jared,
>
>
> many thanks for the suggestion!
> your method works perfect (i only slightly modified dir for input file)
>
>
> 2014-09-19 20:19 GMT+02:00 Sampson, Jared :
0 Jed Goldstone :
> You could extract the flexible residues into one multistate object and use
> show all_states. So, you'd only be dealing with 2 objects - Ca and residues.
>
> Jed
> On Sep 21, 2014 3:23 AM, "James Starlight" wrote:
>
>> Dear Pymol users!
&
I should to specify that I ask this because normally VMD didn't produce
multi-state pdb from the md trajectory so it seems I need to use some
plugin to load *.dcd or *.trr
James
2014-09-22 13:53 GMT+04:00 James Starlight :
> Hi Jed,
>
> so this method is working of the ensem
Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared :
> Hi James -
>
> On Sep 22, 2014, at 4:30 AM, James Starlight
> wrote:
>
> Hi Jared,
>
>
> many thanks for the suggestion!
> your method works perfect (i only slight
some additional question about shell scripting (copied from the amber forum
because I'd like to find as more sollutions of this problem as possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
of the
ligand (which is the RES in pdb) and add after this line TER record. E.g
the basic idea:
grep -v "ATOM.*\(RES\|MOL\)" $pdb | # smth with sed > pdb_with_TER.pdb
now I only would like to know proper reg expression in my case for GREP and
command for SED
James
2014-09-
de the N-ter and C-ter from your
> calculations, or they will completly flatten your spectrum.
>
> Cheers,
> Gian
>
>
>
>
> On 9/21/14 9:19 AM, James Starlight wrote:
>
>> Dear Pymol users!
>>
>>
>> In this topic I've decide to put all questi
Dear Pymol users!
Typically when I'm looking at the ligand binding sites (present->show of
the receptor-ligand.pdb complexes all receptors non-canonical residues or
the different titrable forms of the standard ones (e.g HIP-protonated HIS
or ASH- protonated ASN) are recognized as the ligands as we
Dear PyMol users!
I'm writing of some automatic script aimed on the embedding of the
receptors into the membrane consisted of the pre-equilibrated lipids as
well as hole for the protein. The main issue that some of the receptors
consist of the bulky PHE or TRP side chains on their surface which ar
Dear Pymol users!
For better visualization of the MMGBSA outputs from MD performed for 10 ligands
agains 1 receptor-target I wonder to map per-residue decomposition
data from each of the systems onto the receptor's 3D structure.
Eventually I'd like to produce 10 cartoon diagrams which would differ
e trouble.
>
> Regards,
> Osvaldo.
>
> On Wed, Apr 8, 2015 at 1:47 PM, James Starlight
> wrote:
>>
>> Dear Pymol users!
>>
>> For better visualization of the MMGBSA outputs from MD performed for 10
>> ligands
>> agains 1 receptor-target I wonder t
print what pdb and what DAT will be used within this loop
echo ${Logs[i]}
echo ${Complexes[i]}
# here run pymol using i pdb with corresponded i dat !!
#done
I will be thankful for any ideas in the last part of that script!
James
2015-04-09 16:15 GMT+02:00 James Starlight :
> thanks fo
for just that purpose: to make selections
> based on the b-factor value.
>
> color red, b > 0
>
> Cheers,
>
> Tsjerk
>
> On Fri, Apr 10, 2015 at 5:19 PM, James Starlight
> wrote:
>>
>> some specification regarding B-factors visualization for my task:
>>
( byres ( ss )<--
Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ss )<--
James
2015-04-12 15:12 GMT+02:00 James Starlight :
> Hi Tsjerk,
>
>
> the interesting option for coloring which I found to set sensitivity
> of the visualization in my case:
>
>
i, Apr 10, 2015 at 4:48 PM, James Starlight
> wrote:
>>
>> Dear Pymol users!
>>
>> Here I will ask some question regarding visualization issues in pymol.
>>
>> 1- Using ray_trace_mode, 1 I need to decrease at least twisty width of
>> black countour line
Dear Pymol users!
I need to add a few strings to my simple bash script which will creat
a list of pdb files and than will call pymol without GUI from the
terminal to fetch all the pdbs and save it to the desired location.
For one pdb it should be smth like
pdbs="1f88"
pymol -c -q -d "fetch ${pdb
will need to process each of the pdb- e,g to
remove from them ligands or water etc
Thanks!
2016-04-27 12:18 GMT+02:00 James Starlight :
> Please give me an example of the list of 3 pdbs instead of cat $1 as
> well as how to save syntax of how to save each pdb
>
>
> Thanks!
>
> J
!
#mkdir ${pdb_array_store}
for i in `cat ${pdb_array}` ; do wget
http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
done
result
cat: 1UBI: No such file or directory
2016-04-27 12:29 GMT+02:00 James Starlight :
> Please give me an example of the list of 3 pdbs instead of just cat
here might be an error here?
Thanks!
2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar :
> Hi,
>
> You need
>
> for i in ${pdb_array[@]}
> do
> ...
> done
>
> Cheers,
>
> Tsjerk
>
> On Apr 27, 2016 4:44 PM, "James Starlight" wrote:
>>
>&
posed structure as the outcome of
each for loop run ? In other words I need only to save
${pdb_tit}_superimposed.pdb with the lowest RMSD value assuming that
the operation was repeated 3 times for 3 different refs.
Thanks for help!
J,
2016-04-28 15:48 GMT+02:00 David Hall :
> You need to add “,async
Dear Pymol users!
I am in charge with the analysis of protein-protein association during
long molecular dynamic simulation. In particularly I am interesting to
find residues on one of the protein which are crustal for the binding
interface established during Md.
For that purpose I am trying to use
zation?
J.
2016-05-12 12:52 GMT+02:00 Tsjerk Wassenaar :
> Hey :)
>
> That's been a choice of the author. You can contact him and ask.
>
> Cheers,
>
> Tsjerk
>
> On May 12, 2016 12:25, "James Starlight" wrote:
>>
>> Ok, thanks!
>>
>>
Dear Pymol users!
After some post-processing of MD simulation I have extracted from the
traejctory several snapshots as individual pdbs which I need to
1- to re-assign information regarding chain letters (which was lost
after some operations on pdbs) for all of those structures assuming
that wit
M), chain="L"
Alter: modified 511 atoms.
PyMOL>alter (bound_combined and chain N), chain="M"
Alter: modified 433 atoms.
So each step we rename chain i to the i-1 name within given model :)
Thanks!
J.
2016-05-23 19:11 GMT+02:00 James Starlight :
> Dear Pymol users
Dear Pymol users!
I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which consists of 20
snapshots acco
Dear Pymol Users!
Within the Pymol session I have 2 loaded superimposed objects:
1) one experimental pdb consisted of protein with cofactors (ligand and metals);
2) ensemble of 20 md snapshots of the same proteins superimposed on
each others without any cofactors;
For my particular task I need
1
Dear Pymol Users!
Here I desice to continue my topic regarding scripting in Pymol;
My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly
Dear pymol users!
I need to estimate how the side-chains dynamics are differs in MD
compared to X-ray structure.
Assuming that I have 2 structures one from md and another from X-ray
and I select Sidechains from the both as obj1 and obj02
select xray &! n. n+ca+c+o
select md &! n. n+ca+c+o
now tr
Dear PyMol users!
Using present -> ligand sites context menu I would like to display
possible non-covalent contacts between ions embedded within the
protein.
First I tried to rename ATOM to HETATM record corresponds to ions
however pymol still don't recognize ions as ligand.
Will be very thankfu
Dear Pymol Users!
In my work dir I have 200 pdb files of GPCRs and one receptor
reference.pdb (it consist of only one GPCR monomer - seven
transmbembrane scaffold).
I need to write a simple script which will do the following things:
1 - allign (in loop) each structure against reference.pdb using
$ python setup.py
File "setup.py", line 10
print 'Warning: could not import version'
^
2017-07-18 19:37 GMT+02:00 James Starlight :
> Hi Thomas,
>
> could you also send the same script but just with the Super command
&
n)
>
> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>
> Cheers,
> Thomas
>
>> On Jul 18, 2017, at 1:39 PM, James Starlight wrote:
>>
>&
if just add strings in pymol's cmd the "Super version" of the script
works fine so the problem is indeed in MAC :)
2017-07-18 20:53 GMT+02:00 James Starlight :
> There were some errors in the executing pymol script with your commands using
> @ script.pml
> or
> run scri
hello there,
As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (whic
t;
> Hope this helps.
>
> Cheers,
>
> Ali
> ____
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and
Dear Pymol Users,
that is not very related to pymol question but however probably it can
be solved via pymol as well ;-)
I am looking for some script (e.g. via running in pymol no-gui), which
will count the number of standard amino acid residues in the given
PDB. E.g. for particular pdb consisted
i James -
>
> Do any of the options from this previous BB discussion help?
>
> https://sourceforge.net/p/pymol/mailman/message/28466955/
>
> Cheers,
> Jared
>
>
> On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com)
> wrote:
>
> Dear Pymo
ide of my shell script)
пн, 24 июн. 2019 г. в 16:25, James Starlight :
>
> Thank you, Jared!
> how do you think would it be possible to run this command from no-gui pymol?
>
> pymol -c -d "
> from pymol import cmd
> print len( set( [(i.chain,i.resi,i.resn) for i in
-Q option which suppresses all of PyMOL's normal output, as
> well as -k, which prevents it from loading the .pymolrc file (for speed,
> mostly). Also note the quotes in the `sel` variable assignment must be
> single quotes to avoid closing the shell string.
>
> Hope that helps.
ti_0434.pdb"
> LENGTH=$(pymol -cQ -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> ")
> ```
>
> Hopefully that works, or at least gives you an idea of h
Dear Pymol Users!
I need to process input PDB via pymol (this time no need to do it via
no-gui mode!!) to remove chain id from PDB.
I am using alter command to do it with the following syntax
#rename chain A to phantom chain :-)
alter (chain A),chain=''
the problem that in my initial PDBs there
F G )
for i in "$chains_array[@]}"; do
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.save('${output}/output_$i.pdb','all')
"
done
would it be possible rather to make an array and loop inside the
27;chain ' + chain, 'chain=""')
> cmd.save('output_' + chain + '.pdb')
> cmd.delete('*')
> ##
>
> Then run it with PyMOL:
> pymol -ckqr example.py
>
> See also:
> https://pymolwiki.org/index.
;${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
# close the loop and save final output as 1 pdb
cmd.save('${output}/output_withoutAB.pdb','all')
"
вт, 25 июн. 2019 г. в
alter('chain ' + chain, 'chain=""')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join(chains_array) + '.pdb')
now the question would it be possible to do the sam
quot;
вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
>
> If you want to rename multiple chains at once, make a selection like (chain
> A+B+C). This list selection syntax is documented here:
> https://pymolwiki.org/index.php/Property_Selectors
>
> cmd.load(pdb)
> cmd
ot;]
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
"
ot;B"], like in my
example?
вт, 25 июн. 2019 г. в 17:22, James Starlight :
>
> I actually tried to do like that still defining chains_array = ["A",
> "B"] inside of pymol script and use external bash loop to loop over
> pdbs
> but it does not works ;(
>
&g
f you want to remove all the chain IDs (which it appears you
> might), you don't need a list of chains at all, and can just do:
>
> ```
> alter all, chain=''
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On June 25, 2019 at 11:48:32 AM, James St
Dear pymol users!
I am trying to set transparency based on the secondary structure using
pymol selection algebra
# set transparency to all helix and sheets but not loops
set cartoon_transparency, 0.5, ss H+S
which produce the following output
PyMOL>set cartoon_transparency, 0.5, ss H+S
Setting:
sele
> >
> > Something to do with selection based transparency settings not enabling
> > newer ones to be made
> >
> > Cheers,
> >
> > Ali
> >
> > On 26/6/19, 6:18 pm, "James Starlight" wrote:
> >
> >Dear pymol users
Dear Pymol users!
I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.
Here is model of my script
ave.py
remarkably when I use in this GUI session just a command 'save_sep' it
saves the files within the same directory (Which is ok!)
however cmd.extend('prefix', save_sep)does not work :(
чт, 27 июн. 2019 г. в 11:48, James Starlight :
>
> Dear Pymol users!
>
> I
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