Re: [PyMOL] which PyMOL to open?

2017-04-21 Thread Jed Goldstone
The 3D stuff (Zalman, etc) is only if you're using 3D glasses. I typically
use the Tk + console option that opens two windows (the GUI and a
pythonesque console).

Jed

On Apr 21, 2017 2:16 PM, "AJ Vincelli"  wrote:

> Hello all,
>
> I hate to ask a dumb question, but I need some seriously novice help. I
> just installed educational-use-only PyMOL (version 1.7.4.5, x64) on a
> WIndows 10 machine, and I'm trying to open the program from the Windows 10
> start menu. However, there are many choices! Does anybody know what the
> difference is between these options (like Tcl-Tk, Console, Quad buffer,
> Dynamic, etc.)? Or is there a handy webpage that explains the difference? I
> can't find anything in the Wiki or FAQ websites.
>
> Screenshot is attached and embedded here:
>
>
> Thanks!
>
> AJ
>
>
> 
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Re: [PyMOL] (no subject)

2017-04-04 Thread Jed Goldstone
Try using

remove not alt +A

to remove alternative conformations.

Jed

On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <
vivienschoonenb...@gmail.com> wrote:

> Hi there,
>
>
>
> I’m saving the sequences from each chain of the PDB via pymol with
>
> >>save something.fasta, chain A
>
>
>
> This is the same sequence that is shown in pymol and seems to correspond
> to the structure I am looking at.
>
> However, when I loaded new B-factors in my structure, I noticed something
> funny happened. The list which I made corresponding to the sequence I saved
> earlier was too short.
>
> I  found out by iterating that some residues repeated themselves(>>iterate
> (chain A and n. CA), print resn). They carry the same residue number, and
> are not shown in the sequence. However, when I load my B-factors my list
> shifts because of these repeats, making it too short for the complete chain
> and loading the wrong value onto residues.
>
>
>
> Does anyone know why this happens and how I can fix this?
>
>
>
> Thank you,
>
> Vivien
>
> 
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Re: [PyMOL] electrostatic potential as cartoon?

2017-01-05 Thread Jed Goldstone
Vincent,
You could use data2bfactor.py and then "spectrum b" to color residues in 
cartoon settings.
https://pymolwiki.org/index.php/Color
(data2bfactor from Robert Campbell's script repository:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Jed


On 1/4/2017 11:05 AM, vincent Chaptal wrote:
> Hi everyone,
>
> is there a way to color by electrostatic potential but display the
> structure as cartoon?
>
> a workaround could be :
> color white, molecule
> color red, resn asp+glu+thr+ser  etc..
> color blue, resn arg+lys
>
> ... but this seems rather flimsy.
>
> Thank you and best wishes for the new year.
> Vincent
>
>
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>
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>
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>
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Re: [PyMOL] coloring based on alignment

2015-10-28 Thread Jed Goldstone
Vaheh,
You can modify the b-factor column, and color by b-factor. I have used
various value-to-bfactor scripts, with different measures of alignment
similarity.

The one problem I've had is extending the Ca color to the rest of the
residue in stick mode.
Jed
On Oct 28, 2015 3:34 PM, "Oganesyan, Vaheh" 
wrote:

> Colleagues,
>
> Was wondering if there is a functionality built  in PyMOL for coloring of
> the molecule based on sequence identity/similarity? This topic was
> discussed briefly in 2007 and the answer was from Robert Campbell
> suggesting using his scripts. Seems to be a good tool to have for anyone.
>
>
> Regards,
>
> Vaheh Oganesyan
> MedImmune, ADPE
> www.medimmune.com
>
>
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Re: [PyMOL] Pymol Mobile viewer?

2014-10-14 Thread Jed Goldstone
I too would use an Android mobile version to show people a 3D view of 
things while at meetings etc. I've seen people beginning to put tablets 
up next to scientific posters to show more than can be printed in 2D.

I would certainly use it for scientific discussion in all sorts of venues.

I would be willing to pay for it; however we don't have enough PyMol 
users here to justify a site license, and we don't (yet) teach a course 
that would require it.

Jed

On 10/14/2014 1:33 PM, Thomas Holder wrote:
 Hi Doug,

 this is really useful feedback, thanks a lot.

 Cheers,
Thomas

 On 14 Oct 2014, at 02:45, Douglas Houston douglasr.hous...@ed.ac.uk wrote:

 Hi Thomas,

 Although I have no use for the iPad version I can answer your
 questions as if for an Android version.

 In my experience most people have quite a '2D' approach to molecular
 design, due to a lifetime of learning via lectures, journals and
 textbooks. Very often I find myself wishing I could show them a 3D
 representation of whatever it is we're talking about, without having
 to always lug my laptop around with me.

 So I would use it both for teaching and for aiding scientific
 discussion during project meetings, and also to aid in my thinking
 processes when I'm presented with dead time (e.g. on trains, planes
 etc.). I think under those circumstances some reduced functionality
 (esp. in the fanciness of graphics, moveiemaking etc.) wouldn't be a
 problem (although I'd want to keep all the Builder functions,
 including Sculpt and Clean).

 I would be willing to pay for it (in fact I would get the University
 to buy an Institute license so everyone, including students, could use
 it).

 cheers,
 Doug



 Quoting Thomas Holder thomas.hol...@schrodinger.com on Mon, 13 Oct
 2014 18:21:14 -0400:

 Hi Doug,

 to answer your question, Schrödinger is not working on an Android
 version of PyMOL and we don't have plans to start this any time soon.

 But we are happy to collect feedback that will help us prioritize an
 Android port. For those who have an iPad: What do you use Mobile
 PyMOL for? How often do you use it? Did you only install it because
 it's for free or would you be willing to pay for it? Would you pay
 for an Android version? Does the limited interface and reduced
 functionality (compared to desktop PyMOL) satisfy your needs? If
 not, which critical features are missing for you?

 Cheers,
   Thomas

 On 11 Oct 2014, at 06:08, Douglas Houston douglasr.hous...@ed.ac.uk wrote:

 Hi,

 Sorry to dig up such an old thread, but now development time has been
 found for an iPad version of Pymol, can we hope for an Android version
 to appear at any point in the future?

 cheers,
 Doug

 Re: [PyMOL] Pymol Mobile viewer?

 Jason Vertrees Sun, 17 Jan 2010 06:48:31 -0800

 Tsjerk,

 Warren and I discussed this months ago.  While not really a great way
 to spend development time, it would be fun to see PyMOL on one of the
 mobile devices.  In the meantime, check out Molecules
 (http://www.sunsetlakesoftware.com/molecules) the only 3D molecular
 viewer for mobile platforms that I'm aware of.


 Thanks,

 -- J

 On Sun, Jan 17, 2010 at 5:20 AM, Tsjerk Wassenaar
 tsje...@gmail.com wrote:
 Hi Jason,

 Now what will come first? Pymol viewer for Android, for Mobile Windows
 or for iPhone? Would be so cool to show off at a conference, and use
 multi-touch to operate :p

 Cheers,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist

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[PyMOL] combining multiple objects into one multistate object

2014-01-16 Thread Jed Goldstone
I know this seems silly, but I can't figure out how to combine multiple 
separate objects into one multistate object. I have a set of Modeler 
models loaded from a single pdb file, automagically separated into 
separate objects that have been aligned, and I want to combine them into 
one object in order to run Robert Cambell's rmsf_states script (and, 
also since it's just easier to compare and manipulate).

I've searched the manual, the sourceforge list, and the wiki. Somehow 
the command 'create' with 'target_state=-1' and 'discrete=1' seems like 
it should do this, but all the objects end up in the first state (and 
the cartoon representation is a subset of what it should be (other 
representations are fine).
I'm using incentive v1.6.0.0 on Windows 7.

Jed

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Re: [PyMOL] combining multiple objects into one multistate object

2014-01-16 Thread Jed Goldstone
Thanks! That works. I kept trying to avoid writing a script, figuring 
that it should just be an option in 'create'. That is, if the selection 
old_obj has a wild card, then

create new_obj, old_obj*,1,-1
should work. Clearly not; could this be a future feature?

Jed



On 1/16/2014 10:56 AM, Jason Vertrees wrote:

Jed,

You are correct in that you should be using the create command:

# creates new_obj from old_obj1 by copying old_obj1
# in state 1 to new_obj in state 1

create new_obj, old_obj1, 1, 1

# creates new_obj from old_obj2 by copying old_obj2
# in state 1 to new_obj in state 2

create new_obj, old_obj2, 1, 2

# creates new_obj from old_obj3 by copying old_obj3
# in state 1 to new_obj in state 3

create new_obj, old_obj3, 1, 3



If you have any empty session, this will automate the process:

python

for x in cmd.get_names():

  cmd.create(combined_models, x, 1, -1)

python end

Cheers,

-- Jason



On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu 
mailto:jgoldst...@whoi.edu wrote:


I know this seems silly, but I can't figure out how to combine
multiple
separate objects into one multistate object. I have a set of Modeler
models loaded from a single pdb file, automagically separated into
separate objects that have been aligned, and I want to combine
them into
one object in order to run Robert Cambell's rmsf_states script (and,
also since it's just easier to compare and manipulate).

I've searched the manual, the sourceforge list, and the wiki. Somehow
the command 'create' with 'target_state=-1' and 'discrete=1' seems
like
it should do this, but all the objects end up in the first state (and
the cartoon representation is a subset of what it should be (other
representations are fine).
I'm using incentive v1.6.0.0 on Windows 7.

Jed

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Re: [PyMOL] How to automate RMSD calculation for large no of structures

2014-01-07 Thread Jed Goldstone
Check out Robert Campbell's Pymol script repository.
I think align_all_to_all.py should do what you want, including exporting 
RMSD values.

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Jed


On 1/7/2014 11:58 AM, Om Shiv wrote:
 Hello All

 I am a new user to Pymol and Python.

 I have a PDB Structure with single chain (A) and I have modeled 500
 single point mutants of this wild structure.

 Now for each such 500 modeled structures, I would like to calculate RMSD
 (ALL ATOMS) with the wild type PDB structure.

 Can anybody help me with the script to automate calculation of 500 RMSD
 calculations using PYMOL ?

 Secondly, what threshold value of RMSD can be considered above which we
 can say that the mutant structure is considerably different than the
 wild type ?

 Thanks in advance.


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[PyMOL] Caver 3.01 with Pymol 1.6.0.0 on Windows 7

2013-11-07 Thread Jed Goldstone
I just upgraded to Pymol 1.6.0.0 on Windows 7, and Caver 3.01, which 
worked nicely on Pymol 1.5, has stopped working. I've appended the error 
message below. Has anyone else had problems with the Caver 3 plugin? Can 
anyone decipher the Tk callback? I know what the 'no such file' error is 
- there is no output generated.

Thanks,
Jed

java -Xmx500m -cp C:/Program Files (x86)/Caver3/lib -jar C:/Program 
Files (x86)/Caver3/caver.jar -home C:/Program Files (x86)/Caver3 -pdb 
C:/Users/Jed/modeling/caver/caver_output/6/inputs -conf 
C:/Users/Jed/modeling/caver/caver_output/6/inputs/config_2013-11-07-11-58.txt 
-out C:/Users/Jed/modeling/caver/caver_output/6

Error: 1
type 'exceptions.IOError' Exception in Tk callback
   Function: bound method AnBeKoM.details of 
pmg_tk.startup.Caver3_0_1.AnBeKoM instance at 0x0B5C0B08 
(type: type 'instancemethod')
   Args: ()
Traceback (innermost last):
   File C:\Program 
Files\PyMOL\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 1747, in 
__call__
 return apply(self.func, args)
   File C:\Program 
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py, line 634, in 
details
 fc = self.loadFileContent(%s/warnings.txt % (self.out_dir))
   File C:\Program 
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py, line 638, in 
loadFileContent
 handler = open(file)
type 'exceptions.IOError': [Errno 2] No such file or directory: 
'C:/Users/Jed/modeling/caver/caver_output/2/warnings.txt'

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Re: [PyMOL] Set values for dihedral angles

2012-01-26 Thread Jed Goldstone
James-

I think you need to seriously consider using software that's actually 
designed to compute and refine protein models, such as Modeller. There 
are forcefield and structural constraints that PyMol is just not 
designed to do, and your results may not have the scientific validity 
you require.

Jed

Thomas Holder wrote:
 Hi James,
 
 the modeling capabilities of PyMOL are rather limited, there are 
 probably more powerful tools for such tasks.
 
 Without guaranty that the result will be reasonable, try this:
 
 # lock all but the STG tripeptide
 protect not pepseq STG
 
 # 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.
 
 Cheers,
Thomas
 
 James Starlight wrote, On 01/26/12 13:45:
 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  changing dihedral of this 
 amino acids. When I've tried make it by means of DYNOPLOT plugin the 
 rest of the alpha helix was distorded.

 Is there any possible ways to make this conversion ?

 James
 

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Re: [PyMOL] RMSD calculation sans alignment

2011-07-22 Thread Jed Goldstone
Tom-

Try ProFit
http://www.bioinf.org.uk/software/profit/

Jed

Thomas Grant wrote:
 Dear all,

 I'm attempting to align a series of structures using the CEAlign 
 plug-in in PyMOL due to a lack of any detectable sequence homology. 
  CEAlign does a good job of aligning and the fits are very reasonable. 
  However, the RMSD that is calculated is based only on the c-alphas 
 that were actually aligned, not based on the total number of c-alphas 
 in the structure.  After searching online I have been unable to find 
 any software or servers that will simply calculate the RMSD of two 
 structures as is, without aligning them first.  I would think this 
 would be a relatively straightforward thing to do, just to calculate 
 RMSD from two existing structures without translation or rotation for 
 alignment.

 Does anyone know of a way either in PyMOL or in general to simply 
 calculate the RMSD between all c-alphas of two structures?  Obviously 
 it won't necessarily be a one-to-one ratio of c-alphas, but I can 
 manually curate the pdb to include only the equivalent and aligned 
 residues, even if not used in the CEAlign algorithm, so that there are 
 the same number of c-alphas in both structures.

 Thank you for any help and suggestions,

 Tom
 

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Re: [PyMOL] Logging the sculpt wizard

2011-03-23 Thread Jed Goldstone
You might want to try using Modeller instead.
http://www.salilab.org/modeller/wiki/Mutate%20model
It does higher level modelling.

Jed

Martin Hediger wrote:
 Dear List
 I'm trying to automate the following sequence of steps in a PyMOL python 
 script:
 1. Start the mutagenesis wizard
 2. Mutate a reside according to an input from the script (some integer 
 to specify the id)
 3. Apply and close the mutagenesis wizard
 4. Start the Sculpt Wizard
 5. Fix all coordinates but the residue just mutated
 6. Start the sculpt algorithm to get a rough optimization of the side chain
 7. End the sculpt algorithm and close the sculpt wizard.
 8. Save the structure to a new file.

 I have the steps up to 3. ready in a script for generation of variants.
 However, when running a log file while performing steps 4. onwards, 
 there are no commands written into the log file for the sculpting 
 functions. Pressing the Sculpt button in the PyMOLX11Hybrid does not 
 lead to a command I can see in the log file.
 What would be the Python code to start the sculpt process?

 Any hints are welcome.

 Thanks a lot.



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Re: [PyMOL] CASTp plugin

2011-03-22 Thread Jed Goldstone
I had the same problem.
Email Joe Dundas jdunda1 at gmail  for the .py source code .py file, 
and drop it into the modules/pmg_tk/startup folder.

Jed

Hongbo Zhu wrote:
 Hi, Tomas,
 Usually, the Bad magic number is caused by wrong python version when 
 running .pyc file (the .pyc must have been compiled using a different 
 version of python than the one in PyMOL 1.3, which is python 2.5.4). 
 Maybe you have also noticed on the first line of the CASTpyMOL webpage :

 To use CASTpyMOL version 2, you must be using PyMOL version 0.99 

 pymol 0.99 and pymol 1.3 uses different versions of python.

 Maybe you should contact the CASTpyMOL people to get a .py file so you 
 can try them with your pymol 1.3, or ask them to compile a .pyc using 
 python 2.5.4 for you. Or install pymol 0.99 in parallel to you pymol 1.3.

 good luck!
 hongbo

 On 03/22/2011 11:03 AM, Tomáš Kučera wrote:
   
 Hello pymol users,

 I try to install this castp plugin:
 http://sts.bioengr.uic.edu/castp/pymol.php
 -  http://sts.bioengr.uic.edu/castp/infoPages/CASTpyMOL_v2.pyc

 I have pymol 1.3 (windows7 64bit)

 and I got:

 ImportError: Bad magic number in C:\Program Files
 (x86)\PyMOL\PyMOL/modules\pmg_tk\startup\CASTpyMOL_v2.pyc
 Error: unable to initialize plugin 'CASTpyMOL_v2'.

 Does anyone have any idea how to fix this issue?

 Thanks, Tomas

 

   

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[PyMOL] using pymol on a remote server

2010-10-29 Thread Jed Goldstone
I have been thinking about getting a multicore remote server to run 
Autodock, do rendering, etc. It would be convenient to run PyMol 
directly on the server, tunneling the connection to an X-server running 
on my desktop. However, there is a long response-time delay when using 
PyMol 1.2r1 (x86_64) on CentOS 5 , an issue I have been ascribing to 
network latency. Am I correct in this assumption?

I note that there was a short discussion thread last year on 
master/slave pymol sessions, using XML-RPC.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06984.html
I'm completely unfamiliar with this, and do not know how to implement it 
(my desktop runs PyMol 1.2r1 on Windows XP). Would this be an 
appropriate solution? Would it work to call remote plugins?

Jed

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Re: [PyMOL] some help

2010-05-26 Thread Jed Goldstone
A multiple sequence viewer incorporating structural information would be 
incredibly helpful, as then I wouldn't have to generate models for 
everything I want to compare substitutions in.

It might be too much to ask of PyMOL to be good at everything, however. 
Perhaps adding the ability to read in alignments from an external 
program (e.g. in aligned fasta format) containing the sequence of the 
structure (or model) to be aligned to would be sufficient?

Jed


Thomas Juettemann wrote:
 Hi Ashok,

 there are several ways to visualise alignments. Here is a nice overview:

 Visualization of multiple alignments, phylogenies and gene family evolution
 James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice
 Jossinet  Geoffrey J Barton
 Nature Methods 7, S16 - S25 (2010)
 http://dx.doi.org/doi:10.1038/nmeth.1434

 To address your question, it is not possible to my knowledge to upload
 a sequence only to PyMOL. Keep in mind that PyMOL is a molecular
 viewer, not a sequence viewer.  If you want to see your sequence, you
 probably would have to create a 3D model of your sequence (e.g. using
 MODELLER).

 However, I think you have an interesting idea. It would be handy to
 sometimes see a given sequence aligned to the structure I am looking
 at.

 Question to Jason (and the community for feedback):
 Would it be possible to write a module that takes one or more
 sequences, aligns  them to a given structure (or set) that is opened
 in PyMOL and shows the aligned sequences in the sequence viewer? This
 feature would be very handy for me when evaluating alignments before I
 run MODELLER.

 Cheers,
 Thomas

 On Tue, May 25, 2010 at 23:13, Ashok Adhikari
 ashok.adhik...@student.unsw.edu.au wrote:
   
 hi,

 do u know how to upload a sequence which is not in PDB. we dnt know the name
 of the sequence and we have only 250 residues we can align with the
 other file. we did that and we can upload those sequences from PDB but now
 we need to upload the original sequence.

 thanks...in advance.

 ashok
 from UNSW

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Re: [PyMOL] PC based docking program!

2010-05-07 Thread Jed Goldstone
Autodock VINA works fine in Windows. The PyMOL Autodock plugin does not, 
however. There are some issues with Windows-based file naming and 
handling that I cannot figure out. The author, Daniel Seeliger, has been 
doing developing on a Linux system and does not have a Windows machine 
for testing.

Jed
Deepangi Pandit wrote:
 Hi Sona:
 You could try Autodock VINA. Please check the link below for details.

 http://vina.scripps.edu/


 Deepa

 On Fri, May 7, 2010 at 7:48 AM, Sona Vasudevan 
 sona.vasude...@gmail.com mailto:sona.vasude...@gmail.com wrote:

 Hello All,
  
 I would greatly appreciate if anyone can suggest a PC based
 docking program for teaching purposes?  I am trying ArgusLab, but
 that seems too unstable.
  
 Thanks much!
  
 Sona

 
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Re: [PyMOL] coordinates

2010-03-22 Thread Jed Goldstone
Of course, you could just use the .pdb file as a text file:

grep CA .pdb | cut -f 2,4,7,8,9

will get you the amino acid number, the amino acid identity, and x,y,z 
coordinates for the CA.

Jed

Jason Vertrees wrote:
 In newer PyMOLs this is as simple as:

 print cmd.get_atom_coords(oneAtom)

 where 'oneAtom' is an object or selection of one atom in PyMOL.

 For example,

 load $TUT/1hpv.pdb
 print cmd.get_atom_coords(A/30/CA);

 -- Jason

 On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
   
 Hi Mohan,

 You can use iterate_state, which would be the pymol approach:

 coords = {}
 iterate_state 1,n. ca,coords[i]=(x,y,z)

 Or you can take a lower level approach; the python one:

 for i in cmd.get_model('n. ca').atom:
  print i.coord

 cmd.get_model builds you a ChemPy model from a given selection. The
 .atom property is the list of atoms. If you want to know what else is
 possible you might want to have a look at the
 properties/attributes/methods defined:

 for i in dir(cmd.get_model('n. ca').atom[0]): print i

 Hope it helps,

 Tsjerk

 Of course neither way would restrict you to plotting...



 On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
 
 hi all:

  could any one tell me how to get the coordinates for a specific atom in
 a particular amino acid using pymol commands

  is their a commant with can list the coordinates for each aminoacid in
 a protein molecule?? \

  kindly clarify, thanking you in advance.


 - mohan
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Re: [PyMOL] coordinates

2010-03-22 Thread Jed Goldstone
Of course you're all correct - Thierry Fischmann already emailed me to 
correct me :)

I hadn't actually tested anything (mea culpa). I was just trying to 
point out for those of us less familiar with python that there were 
alternatives to doing this relatively simple thing outside of pymol.

Apologies to the list,

Jed


Robert Campbell wrote:
 Hi Jed,

 On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote:

   
 Of course, you could just use the .pdb file as a text file:

 grep CA .pdb | cut -f 2,4,7,8,9

 will get you the amino acid number, the amino acid identity, and x,y,z 
 coordinates for the CA.
 

 Often this will work, but unfortunately it is not fool proof.  If there is
 no chain ID, if the residue numbers are greater than 999 or if there are
 alternate position characters present on the atom names, then your field
 counts in your cut command will be off. The PDB file is very strict about
 which character columns contain which information and there is no requirement
 for spaces between those data columns.

 Cheers,
 Rob
   

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[PyMOL] Autodock/Vina Pymol Plugin Windows problem

2010-01-07 Thread Jed Goldstone
I can't seem to get the autodock Pymol plugin to work correctly in 
Windows (XP). I think it's a bug somewhere.
I'm using the latest version of autodock grid and dock, and MGL Tools 
1.5.4 on Windows XP with Python25, and PyMol 1.2r1

I've emailed the author, Daniel Seeliger, but haven't gotten a reply. 
Has any had experience with this?

I'm getting at least 2 different errors:
first, in setting up a receptor. When I click on the PyMOL Selection and 
Generate Receptor I get the following error:

Batch: C:\Program Files\MGLTools 
1.5.4\MGLToolsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r 
C:\Program Files\PyMOL\.ADplugin\receptor.dr1a.pdb -o 
receptor.dr1a.pdbqt -A checkhydrogens
'{' is not recognized as an internal or external command,
operable program or batch file.

second, if I Select as Flexible in the Autodock plugin a PyMol 
selection, I get the following Pymol error in background function,

Error: 1
type 'exceptions.KeyError' Exception in Tk callback
 Function: bound method Autodock.select_flexible_residues of 
pmg_tk.startup.autodock.Autodock instance at 0x10941580 (type: type 
'instancemethod')
 Args: ()
Traceback (innermost last):
 File C:\Program Files\PyMOL/modules\Pmw\Pmw_1_3\lib\PmwBase.py, line 
1747, in __call__
   return apply(self.func, args)
 File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line 
1800, in select_flexible_residues
   receptor_object = self.receptor_dic[rec]
type 'exceptions.KeyError': ''


Jed

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[PyMOL] pymol autodock plugin

2009-08-13 Thread Jed Goldstone
The autodock plugin written by Daniel Seeliger ceased to function (load) when I 
upgraded to Pymol 1.2r1. 
Although it is not compatible directly with Autodock 4, it did have the useful 
functionality of 
presenting an autodock 'box' that was readily tweakable, so that the parameters 
could be exported for
Autodock Vina. I would LOVE to have this resurrected, but I don't know python - 
can anybody help with this?

The specific failures I got were:

File C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py, line 16, in 
module
from Numeric import *
ImportError: No module named Numeric
Error: unable to initialize plugin 'autodock'.


Any help would be greatly appreciated.

Jed

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[PyMOL] fill a cavity with a closed polygon

2008-09-07 Thread Jed Goldstone
Is it possible to fill a cavity (e.g. a CASTp-derived one) with discrete 
spheres (as per the examples on the CASTp site obtained with RasMol) or a
closed polygon (as visualized by ICM) rather than a surface mapped to the
residue surfaces? 
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