ust 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 have a folder with many pdb files. I would like to use pymol in
> n
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
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
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 Starlight (jmsstarli...@gmail.com)
> wrote:
>
>
"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
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')
" > $output/pymol_${pdb_name}.log
done
вт, 25 июн. 2019 г. в 16:58, James Sta
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.alter('chain ' + '+'.join(chains_array), 'chain=""')
> cmd.save('output.pdb')
>
>
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 same but in my bash script?
вт, 25 июн. 2019 г. в
in $i)', 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
# close the loop and save final output as 1 pdb
cmd.save('${output}/output_withoutAB.pdb','all')
"
вт, 25 июн. 2019 г. в 16:14, James Starlight :
>
> thanks so much Thomas, for this example!
>
> Actu
save('output_' + chain + '.pdb')
> cmd.delete('*')
> ##
>
> Then run it with PyMOL:
> pymol -ckqr example.py
>
> See also:
> https://pymolwiki.org/index.php/Launching_From_a_Script
> https://pymolwiki.org/index.php/Python_Integration
>
> Cheers
d.alter('(chain $i)', 'chain=\"\"')
cmd.save('${output}/output_$i.pdb','all')
"
done
would it be possible rather to make an array and loop inside the pymol
to rename all chains into the blank chain during one execution of
pymol?
Thanks in advance!
вт, 25 июн. 2019 г. в 14:50, James Starl
Dear Pymol Users!
I need to process input PDB via pymol (this time no need to do it via
no-gui mode!!) to remove chain id from PDB.
I am using alter command to do it with the following syntax
#rename chain A to phantom chain :-)
alter (chain A),chain=''
the problem that in my initial PDBs there
TH=$(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 how it might be done.
>
> Best,
>
; 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.
>
> Cheers,
> Jared
>
>
>
>
> On June 24, 201
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
> cmd.get_model(sele
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
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
_
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: akus8...@uni.sydney
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
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 <jmsstarli...@gmail.com>:
> There were some errors in the executing pymol script with your commands using
> @
ject=aln
> remove not (byres aln)
>
> 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
hon setup.py
File "setup.py", line 10
print 'Warning: could not import version'
^
2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Hi Thomas,
>
> could you also send the same script but just with the Supe
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
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
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!
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
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
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 <jmsstarli...@gmail.com&g
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
.
2016-05-12 12:52 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> 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" <jmsstarli...@gmail.com> wrote:
>&
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
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 <li...@cowsandmilk.net&
be an error here?
Thanks!
2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hi,
>
> You need
>
> for i in ${pdb_array[@]}
> do
> ...
> done
>
> Cheers,
>
> Tsjerk
>
> On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli..
!
#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 <jmsstarli...@gmail.com>:
> Please give me an example of the
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 <jmsstarli...@gmail.com>:
> 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
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
: 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 jmsstarli...@gmail.com
wrote:
some specification regarding B-factors visualization for my task:
is it possible within the open pymol session
1) to select only
, 2015 at 4:48 PM, James Starlight jmsstarli...@gmail.com
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 (especially in the loop segments).
2- Being
).
Selector-Error: Malformed selection.
( ss )--
James
2015-04-12 15:12 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Hi Tsjerk,
the interesting option for coloring which I found to set sensitivity
of the visualization in my case:
spectrum b, red_orange_white, minimum=-1, maximum=0.1
,
Osvaldo.
On Wed, Apr 8, 2015 at 1:47 PM, James Starlight jmsstarli...@gmail.com
wrote:
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
of that script!
James
2015-04-09 16:15 GMT+02:00 James Starlight jmsstarli...@gmail.com:
thanks for the information! Here I ask to provide me with some more
help because I'm not a big expert in the python .
For instance I have 2 folders- one with 10 pdb's corresponded to the
10 complexes of one
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
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
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
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
2014-09-24 11:06 GMT+02:00 James Starlight jmsstarli
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 questions regarding visualisation.
This time I'm very intresting whether it possible to add some effect
Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
On Sep 22, 2014, at 4:30 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly
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
:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:
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 jared.samp...@nyumc.org:
Hi James -
I don’t have any experience with Profit
Goldstone jgoldst...@whoi.edu:
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 jmsstarli...@gmail.com wrote:
Dear Pymol users!
In this topic
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 jmsstarli...@gmail.com:
Hi Jed,
so this method is working
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
at 10:09 PM, James Starlight jmsstarli...@gmail.com
wrote:
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
10:48 GMT+04:00 James Starlight jmsstarli...@gmail.com:
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 advanced tutorials foruced on the visualization in PyMol
alternatives which could be used as parts of
the shell script.
James
2014-09-15 18:52 GMT+04:00 James Starlight jmsstarli...@gmail.com:
Hey,
I've occasionally deleted my profit script which do superimposition
automatically so I'll be very thankful if someone remind me profit input
script syntax
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
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.
Hope I helped,
Fotis Baltoumas
2014-09-17 13:01 GMT+03:00 James Starlight jmsstarli...@gmail.com
initial 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 for
NAMD but in case of amber its really exist (the structure
structures...
RMS: 7.134
Where I made error?
James
2014-09-12 9:13 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Hi Jared,
yes from pymol it's OK, here I've mentioned about ProFit :) but this also
have been solved. ;)
James
2014-09-11 19:43 GMT+02:00 Sampson, Jared jared.samp
but results were empty.
James
2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:
Hi
Small correction to Gianlucas suggestion
will direct the output to a file, overwriting
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,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi
Thank you very much!
James
2014-09-12 12:36 GMT+02:00 Marko Hyvonen mh...@cam.ac.uk:
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 ^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK
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 jmsstarli...@gmail.com:
Thanks Markus, I'll try to examine it!
Jed,
the main problem with the profit is that I need to superimpose
!
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
Ok, ProFit has been passed :D
Now I'm looking for some software which could do the same least
Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr:
Don't even need cat
simply do
grep PPC ref.pdb tar_i.pdb
redirecting std out with appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
Dear Pymol users!
I've
://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a):
Thomas,thanks for help- I'll try to test your script!
Jed, many thanks too!
if I understood correctly
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\n;
(tarfile, 'tar')
cmd.align('ref', 'tar')
cmd.save(outfile, 'ref')
Then on the command line call it like: python my_align.py reffile.pdb
target.pdb output.pdb
On 09/04/2014 11:06 AM, James Starlight wrote:
thank you very much!
so now only my question regarding the usage of the pymol
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 jmsstarli...@gmail.com
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 jmsstarli...@gmail.com
wrote:
should to add
than I've used both
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
...@gmail.com:
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,
I'll try to use this opportunity
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, James Starlight jmsstarli...@gmail.com
wrote:
Dear PyMol users!
I'd like to find possibilities for running of some
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 jmsstarli...@gmail.com:
Thanks Guys!
I'll check the tutorials.
All the best,
James
2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net
thanks!
and do I need to pipe the below command to smth
grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb
if I need to change 'END' to 'TER' in the merged.pdb ?
2014-09-04 16:54 GMT+02:00 James Starlight jmsstarli...@gmail.com:
thanks!
and do I need to pipe the below
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how
occurs (I have not this in case of ONE model from
the ensemble)
James
2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also
is it working here?
https://www.sendspace.com/file/8i0aqo
James
2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de:
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 upload
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 teva...@gmail.com:
On 27 August 2014 15:43, James Starlight jmsstarli...@gmail.com wrote:
and than how to quick merged aligned conformers back
Dear Pymol Users!
I wounder whether it will be possible to save big ensemble of the loaded
into pymol Pdb's files as the trajectory output (like dcd format) what are
actually can be performed by vmd (e.g by means of
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/).
The
Dear PyMol users!
I'm learning of the python scripting for the solution of typical structural
bioinformatics problems. This time I'd like to integrate in pymol simple
script which will search for the selected motifs (just several amino acids
situated in adjacent positions along the sequence) and
Dear PyMol users!
I've forced with the problem of the installation of AutoDock plugin
pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've
tried to install it manually from the downloaded py script but at the
starting of pymol below error has bbeen appeared
Unable to initialize
are
cations because of the symbol in the last column. By default, PyMOL doesn't
make bonds to cations. But this will work:
PyMOLunset pdb_unbond_cations,
PyMOLload example.pdb
Hope that helps.
Cheers,
Thomas
On 06 Dec 2013, at 11:04, James Starlight jmsstarli...@gmail.com wrote:
Thomas
212-263-7898
http://kong.med.nyu.edu/
On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.com
wrote:
Dear PyMol users!
I'd be thankfull if you provide me with the easliest way how I could save
selection to the separate pdbs. For example I've loaded 10 pdbs
Der Pymol users!
I wounder to know if it possible to increase rendering rate mainly at the
expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in
the hyper-threading mode) I've spend ~ 2 hours to render image consisted
of ensemble of conformations (~ 30 aligned pdbs) using
Dear PyMol users!
I'm looking for python script which would perform the
1- loading ensemble of the pdbs to the pymol (assuming that it could be
done by loadDir script)
2- Perform structural alighnemnt of all loaded structures against reference
0.pdb by means of buit-in TMalighn module
this
are in the startup subdirectory.
Also other plugins are working without complaint.
This is exactly the way the plug was working the last time that I
attempted its installation and use.
On 11/15/2013 03:14 PM, James Starlight wrote:
This issue have been solved. Caver works fine. Does anyone
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
This issue have been solved. Caver works fine. Does anyone tried to include
path information obtained by caver to the NAMD steered md simulation? I'm
looking for the protocol for guiding namd forces along the direction
obtaned from CAVER.
James
2013/11/15 James Starlight jmsstarli...@gmail.com
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 pymol source
would introduce selected mutations in the defined PDB file and produce PDB
output
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
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
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
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
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) ?
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
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
try, after 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 name
like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still
at
once ?
James
2013/3/28 James Starlight jmsstarli...@gmail.com
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
and when I've started
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