Re: [PyMOL] [Help]About indentifying interaction between residues

Hi Nikita - To me this looks like the cartoon representation for missing residues, which is controlled by the cartoon_gap_cutoff setting. If you either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away? Usually the dashed line

[PyMOL] [Help]About indentifying interaction between residues

Dear All, My name is Nikita, I am a graduate student at Academia Sinica, Taiwan. This e-mail aims to ask for help in identifying the bond/interaction between two residues. I am currently learning about PyMol to utilize in my project. I used PyMol to visualize potential H-bond interactions in

Re: [PyMOL] [Help]About using PyMOL for Master's thesis

Hello Haruki, My name is Thomas Stewart and I'm one of the PyMOL developers at Schrodinger. You can use an educational license to fulfill course or program requirements such as a Master's thesis or dissertation. We hope to reword the website in the near future to make it more clear when

[PyMOL] [Help]About using PyMOL for Master's thesis

To whom it may concern, My name is Haruki Soejima and I am studying at the Graduate School of Marine Biosciences, Kitasato University, Japan. The purpose of this e-mail is to ask you a question about the license of PyMOL. I used the “Educational-Use-Only PyMOL” in my study for my Master's

Re: [PyMOL] help with PyMOL rename command

Thank You a lot indeed explanation ways more clear than the wiki one https://pymolwiki.org/index.php/Rename https://pymolwiki.org/index.php/Rename I know I should have tried more Again Thanks___ PyMOL-users mailing list Archives:

Re: [PyMOL] help with PyMOL rename command

Dear wdela, usually each atom in a residue has a different atom name. If this is not the case, the rename command will rename the atoms, that do not have unique names within a residue. It appears as if you cannot specify which atom names the renamed atoms will get. If you want to change to

[PyMOL] help with PyMOL rename command

Hi need help with PyMOL rename command: from https://pymolwiki.org/index.php/Rename : Rename rename creates new atom names which are unique within residues. USAGE CURRENT rename object-name [ ,force ] force = 0 or 1 (default: 0) PROPOSED rename object-or-selection,force NOTES

Re: [PyMOL] Help with selecting interface residues between two structures

chain of base. I understand this. However, why “not /base//H+L” returns an empty selection? Thanks! From: Jarrett Johnson Sent: Thursday, June 29, 2023 6:31 AM To: Zhou, Yingyao Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Help with selecting interface residues between t

Re: [PyMOL] Help with selecting interface residues between two structures

Hi, There might be a cleaner way to do this, but I propose creating a mapping of your chains from base to pred and use the `iterate` command to get the relevant identifiers and map them back to the prediction. Here is a full script that pulls from the PDB that attempts this idea. from pymol

[PyMOL] Help with selecting interface residues between two structures

I am a relatively new PyMOL user and would like to get some helps from the community. I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) . Structure "base" is the experimental true structure, structure "pred" is

[PyMOL] Help superimposing protein and sugar

Hello all, TLDR; What’s the best way to place one molecule over a geometrically similar but unrelated second molecule? I’m a scientist studying the docking of glycans to antibodies. I’m trying to use pymol to position my glycan, a 10-mer called gxm, close to its putative binding site. My

Re: [PyMOL] Help - how mutation affects protein structure

Dear Susanna, in addition to MD calculations I suggest you to perform a check on your mutated protein. Circular dichroism is a simple technique that allows to monitor the global fold of your protein. Mutating a residue may affect the folding and this seems an underestimated problem in the

Re: [PyMOL] Help - how mutation affects protein structure

Hi Susanna, As you can see, pymol allows you to mutate residues. However, in order to assess their influence, you should most likely run MD simulations on both the wild type protein and mutant(s) and compare. Kind regards, Sorin On Tue, Apr 12, 2022, 5:35 PM susanna pagni wrote: > Hello, >

[PyMOL] Help - how mutation affects protein structure

Hello, I am quite new to PyMOL. I would like to assess how an amino acid change might affect the protein structure. I used the Wizard Mutagenesis to change the amino acid of interest but don’t know how I can see how the protein structure is affected by the mutation. Can you please help me

Re: [PyMOL] help - password cracked

Hello, We're aware of this issue, and I believe all EP license holders may have received this warning from Google. However, this can safely be ignored for now. The password students and other users receive just provides access to the PyMOL Educational Product license and nothing there stores any

[PyMOL] help - password cracked

Hey everybody! I may have a problem, maybe it's nothing, but better to be sure. About a week ago, I got a notification from Google that my password to the pymol.org/ep link had been cracked. Since then I've been trying to find any information concerning this problem - mainly in the form of 'how

[PyMOL] Help with modelling metalloproteins.

Hello all, I am an MRes student trying to do some bioinformatics if anyone could help me that would be really appreciated. I have looked to see if my question has been answered and I cannot see the particulars that I am looking for. I used Phyre2 to model the predicted 3D structure for my

Re: [PyMOL] Help ASPB

 Dear Clarisa, > On Sep 10, 2020, at 2:56 AM, Clarisa Alvarez > wrote: > > Dear David > Thank you very much!you do not know how much you helped me!!Thanks! > I have two questions: > - with you sent I only saw lateral chains, how could I see backbone? You want to click on “H” button and

[PyMOL] Help APSB

Dear all, I need your help. I have discrepancies when I applied APBS ramp01 on a selected pocket object generated by myself with the electrostatic potential displayed throughout the protein. Somebody could help me?Why could this be caused? What are the differences between ramp01..ramp01...etc?

Re: [PyMOL] Help ASPB

select pos,(resn arg+lys+his) show sticks, (pos and !name c+n+o) color marine,pos disable pos select neg,(resn glu+asp) show sticks, (neg and !name c+n+o) color red,neg disable neg select neutral, (resn gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe) show sticks, (neutral and !name

[PyMOL] Help ASPB

GenScript Dear all, Thanks in advance. I have this problem, I have two pockets with electrostatic potential made by APSB, does anyone know how I could tell which residue contributes to each potential in each protein? Thanks in advance. Regards, Clarisa.

[PyMOL] help

hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! -- Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of

[PyMOL] Help

Hi! I am new user. >From a 3DRISM analysis 1. I want to show iso-surface of a potential map (.dx) and another 2. explicit distribution (.pdb) which should be colored by index from low to high,(e.g. red to blue). Thanks in advance! -- Vertika Gautam Research Assistant Drug Design and

[PyMOL] [HELP]Unable to import pymol as library

Hi all, I'm new here. My name is Aureliano Guedes. I'd like your help. I was trying to import pymol inside to python script to use to align all-vs-all a list of structures. I have a full pymol's installation working well installed with linux brew. $ pymol --version PyMOL 2.2.0 Open-Source $

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Dear Christoph and David Thanks for the support and solution. The solution given by Christoph solved the issue. Now, the plugin manager is running smoothly. Cheers Vijay On 8/22/17, David Hall wrote: > See https://sourceforge.net/p/pmw/patches/7/ >

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Dear Christoph Thank you for the help. I followed your suggestion, but no success. However, a new line is appearing now at the bottom of the error message, here is the complete error message: Error: 1 TypeError Exception in Tk callback Function: .plugin_manager at 0x01B40CB228C8> (type: )

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Hello, try to uninstall Pmw and reinstall it using Pmw-2.0.1-py3-none-any.whl from . C:\Python36\python.exe -m pip uninstall Pmw C:\Python36\python.exe -m pip install Pmw-2.0.1-py3-none-any.whl Christoph On 8/21/2017 8:27 AM, Vijay Masand

Re: [PyMOL] Help Download structural alignment

Hi Clarisa, you can save an alignment using the create and save commands, e.g.: fetch 1oky 1t46, async=0 as ribbon align 1oky, 1t46 create aligned, all save aligned.pdb, aligned You can also save the alignment in clustalw format, see http://pymolwiki.org/index.php/Align. I hope this is what

[PyMOL] Help Download structural alignment

Hi everyone: I am writing asking help to download the structural aligment performed in pymol. Thanks in advance. Regards, Clarisa. 2016-06-14 11:01 GMT-03:00 : > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net >

Re: [PyMOL] Help for saving movie in png

Hi Pranab, Am 13.11.2015 um 17:00 schrieb Pranab Jyoti Bhuyan: > Can you please tell me how to save a movie as a series of *.png files > from terminal in linux? This can be done with the mpng command. See http://pymolwiki.org/index.php/Mpng Cheers, Christian

[PyMOL] Help for saving movie in png

Hi, I am new learner of PyMOL. Can you please tell me how to save a movie as a series of *.png files from terminal in linux? Thanks & regards Pranab Indian Institute of Science --

[PyMOL] help

Hello everyone: I need help because I have a pdb of a monomer but I know that it is a dimer by crystallographic symmetry, how can I make a new molecule of it? because I could make it by generate/symmetry mate...but I could not save it...any help will be great! Thanks in advance!

Re: [PyMOL] help

Hi Clarisa, If I understand correctly you generate the dimer, but you are not able to save it. Wich error did you get? Did you select all the object when saving the file? By the way, may be you will find this wiki page useful. Cheers, Osvaldo. On Wed,

Re: [PyMOL] help

Clarisa, Depending on what you want to do with the file, you may not need to save a new PDB at all. You could for example, * Issue the command symexp ,,(all),4.0 to generate nearby symmetry mates, then remove the objects you don't need to form the proper dimer. ( is your

[PyMOL] help making a movie

Dear Pymolers, I am looking forward to make a movie for a nucleic acid where I would like to show the opening/bond breaking of several base pairs and interaction with another protein. Is it possible to do this in pymol? Any help regarding this is highly appreciated! Regards Ravi

[PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

Dear Pymolers. I am playing around with creating a pdf file with 3 D graphics. I am saving in *idtf* format, which I convert to *u3d, *and then include in pdf through latex. I can do this on windows, but I can't compile IDTFConverter *on linux 64.* I have made this progress

Re: [PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

On 04/03/13 12:21, Troels Emtekær Linnet wrote: Dear Pymolers. I am playing around with creating a pdf file with 3 D graphics. I am saving in *idtf* format, which I convert to *u3d, *and then include in pdf through latex. I can do this on windows, but I can't compile IDTFConverter *on

[PyMOL] Help with alignments

I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad

Re: [PyMOL] Help with alignments

Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I am wanting to align proteins based on superposition of particular chains. Is it possible to

Re: [PyMOL] Help with alignments/ more general create and align question

. Thanks. From: jason.vertr...@schrodinger.com Date: Tue, 11 Dec 2012 07:38:32 -0600 To: jonat...@strubi.ox.ac.uk CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Help with alignments Hi Jon, align prot1 and chain A, prot2 and chain X

Re: [PyMOL] Help with autodock plugin for PyMOL

What is the atom name of EFP.ligand:A:EFP999? Can you check your pdb file? Do you rename them before running the plugin? Den 26/10/2012 23.26 skrev Ragnar Thomsen rthoms...@gmail.com: I have a problem when running the autodock plugin for PyMOL. I followed the tutorial at

[PyMOL] Help with autodock plugin for PyMOL

I have a problem when running the autodock plugin for PyMOL. I followed the tutorial at http://www.pymolwiki.org/index.php/Autodock_plugin. When I prepare the ligand I get the following error output: Batch: /usr/lib/python2.7/site-

Re: [PyMOL] Help auto interpolate

Hi Anke, we are currently trying to do movies and are running into some problems concerning the “auto interpolate” function of pymol. We realized that camera and molecule positions are always interpolated back to the position of frame 1 at the end of the movie. Autointerpolate is not the

Re: [PyMOL] PyMOL help

Hani, You can these GUI commands: A (Action)---preset---ligand sites or A---find---polar contacts Hope this helps you! Peter syed.abidi skrev 2012-03-19 12:19: Dear All, I have a small query regarding PyMol and I would appreciate if you can help me with it. My query is: How do I

[PyMOL] PyMOL help

Dear All, I have a small query regarding PyMol and I would appreciate if you can help me with it. My query is: How do I analyze interactions with PyMol after I have docked my files? I wanted to know which molecules/amino acids are interacting in the docked confirmation. I would really

Re: [PyMOL] PyMOL help

Hi Hani, with PyMOL you can visualize polar contacts, using the distance command with mode=2 argument. See the PyMOLWiki page: http://pymolwiki.org/index.php/Distance Example: distance interface, chain A, chain B, mode=2 However, this is not really a analysis of the interface. Instead I would

Re: [PyMOL] fink install pymol help

On Mar 15, 2012, at 10:14 PM, Shane Neeley wrote: I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? Short answer: You don't. The fink version of PyMOL is run from the command line. Open up a new

Re: [PyMOL] fink install pymol help

Try  fink install pymol-py27   From: Shane Neeley shane.nee...@gmail.com To: pymol-users@lists.sourceforge.net Sent: Thursday, March 15, 2012 4:53 PM Subject: [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol

Re: [PyMOL] fink install pymol help

shane.nee...@gmail.com *To:* pymol-users@lists.sourceforge.net *Sent:* Thursday, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http

Re: [PyMOL] fink install pymol help

, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get

[PyMOL] Help converting shell script to python

Hi guys. I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms on a win machine. The plugin is dependent on a shell script: pdb_to_xyzrn But I cant execute it on a win machine, and I won't install cygwin. Can someone help me convert the shell script to a python script? Or

Re: [PyMOL] Help converting shell script to python

Case closed. Thanks to Hongbo Zhu for a solution. Best Troels 2011/12/12 Troels Emtekær Linnet tlin...@gmail.com Hi guys. I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms on a win machine. The plugin is dependent on a shell script: pdb_to_xyzrn But I cant

Re: [PyMOL] help needed

Hi Anasuya, I have around 19,200 unique PDB files. Each of them have one or more ligands in it. For each ligand, I have to extract a zone which contains complete residues within 4.5Angstroms of the ligand [ i.e. ZONE1] and then extract another zone, which has complete residues within

[PyMOL] help needed

hi all, I am writing this email with regards to the following problem. Statement of the problem: I have around 19,200 unique PDB files. Each of them have one or more ligands in it. For each ligand, I have to extract a zone which contains complete residues within 4.5Angstroms of the ligand [ i.e.

Re: [PyMOL] Help

Hi Babban, For modeling the polymers you probably want to try a docking program. Maybe HADDOCK suits your needs... Hope it helps, Tsjerk On Sun, Jul 31, 2011 at 1:42 AM, Babban Mia babban...@gmail.com wrote: Dear users, Is there some program to calculate the zeta potential or streaming

Re: [PyMOL] Help

Hi Babban, regarding your questions on peptide building: My last doubt is about creating polymers out a given PDB ? I am studying the fibrils of some proteins and although the structure of fibril is not know but through some analysis I have come to understand the region in peptide which is

[PyMOL] Help

Dear users, Is there some program to calculate the zeta potential or streaming potential of protein molecules (PDB files ) Is there some program to calculate the dipole moment of protein molecules at different PH values? My last doubt is about creating polymers out a given PDB ? I am studying

[PyMOL] Help for surface coloring

Dear community, I was searching the internet for several days now to find out how to perform a distance dependent coloring in pymol. The idea is to color the surface of a viral (spherical) structure. I would like to define the xyz-coordinates of the center of the viral structure an color all

Re: [PyMOL] Help for surface coloring

Hi Robert, you can set the distance between each atom and the center as b-factor, and then use spectrum (or spectrumany [1]) for coloring. I wrote a small python script that will do that, see attachment. Example (in PyMOL command line): run distancecoloring.py centerdistance2b (all)

Re: [PyMOL] Help for surface coloring

Hi Robert, I did something like this in the past. Check out the ramp_new command page on the PyMOLWiki for an example (http://pymolwiki.org/index.php/Ramp_new#Elaborate_examples) for arbitrary functions. Here's a very quick way to color a surface by distance from a given point--here I chose the

Re: [PyMOL] Help for surface coloring

I have a slightly different answer using (almost:) only PyMOL commands: # take 1acb as example fetch 1acb, async=0 import numpy # center is [x0,y0,z0] x0,y0,z0=[1,2,3] alldist = [] iterate_state 1, 1acb, alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2]))) # assign dist to

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Thanks Rafael and Jason, I upgraded to the latest driver version for Linux i.e 275.19 and now have stereo working with some caveats. I am running the PLANAR SA2311 at 120 Hz and 1920x1080 resolution and the stereo is rather finicky with the nvidia 3dvision setup. I see a lot of random stereo

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hello Hari, I had some flickering problems when I first tried the stereo mode on an Alienware LCD display. There is one option in the Nvidia driver that seems to keep the display at 60Hz, it is called Force Full GPU Scaling. Make sure that the option is turned off, otherwise you won't be able

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Thanks a tonne Marc . Turning OFF Force Full GPU scaling in the DFP-0 and DFP-1 settings of the n-vidia-settings panel made all the difference. Once I unchecked that box it made the stereo stop flickering and switching from coming at you to going away from you ( i.e flipping). Stereo with the

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, I'm glad that worked for you. I contacted Planar and they also had a few hints for us: I have heard of synch issues with the Quadro FX3700 in Windows XP, so there could be an issue in Linux as well.  Here are a few ideas to try out: 1. We found that connecting the 3-pin mini-din

[PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi, I am using the nvidia driver : 195.36.24 OS: Ubuntu Lucid lynx 10.04 , 64 bit I have a working xinerama config with two LCD screens one a regular dell LCD at 2560x1600 and the other a stereo capable PLANAr LCD at 1920x1080. Both screens were configured to near working stereo based on the

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, According to the NVidia's website, the Planar SA2311W is compatible with 3DVision since the version 260.19.36 of the Nvidia's video driver. Apparently the driver you're using is a way too old . Rafael. On 7/20/11 6:41 PM, hari jayaram wrote: Hi, I am using the nvidia driver :

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, Please update your driver and ensure that your monitor's refresh rate is 120 Hz. Cheers, -- Jason On Wed, Jul 20, 2011 at 12:41 PM, hari jayaram hari...@gmail.com wrote: Hi, I am using the nvidia driver : 195.36.24 OS: Ubuntu Lucid lynx 10.04 , 64 bit I have a working xinerama

[PyMOL] PyMOL Help

Hi PyMOL, This may be a very simple problem to solve. How do I select chain-specific individual residues in the command line? For example: 1PSO.pdb has two chains: E and I. If I enter [select catalytic, resi 2] I get the residue I want selected BUT i also get residue 2 in the I chain selected -

Re: [PyMOL] PyMOL Help

Hi Matthew, You can specify a chain with chain X or the abbreviated c. X where X is the chain identifier. In your case, # select residue 2 from chain E select catalytic, resi 2 and chain E # same as above select catalytic, i. 2 and c. E For more help, see the PyMOLWiki

[PyMOL] help with moving objects separately

I am trying to create a view of a homomultimeric protein by duplicating the structure of its subunit and rotating them around a central axis. I am finding this difficult as the commands don't always behave as I expect them to. Can you tell me the best commands to use in this task. For

Re: [PyMOL] help with moving objects separately

Mary, The duplication idea was correct, but most likely needed to be done via the command line for flexibility: duplicating a single object of two+ chains results in an object of two+ chains. Thus, calling rotate on the new object will rotate both chains in the new object. If you want to just

[PyMOL] Help Needed

Dear Sir, I, Kousik Kundu, am a Ph.D student at university of Freiburg, Germany. I am using Pymol for my recent work. I need to to the amino acids involve in an interaction. For example 1BM2 (PDB id) is a complex of a SH2 domain and a small peptide. Here i want to know which amino acids

Re: [PyMOL] Help Needed

Dear Kousik, Sue Jones PROTORP server should do the trick: http://bioinformatics.sussex.ac.uk/protorp Cheers, Thomas On Wed, Dec 9, 2009 at 14:57, Kousik Kundu kou...@informatik.uni-freiburg.de wrote: Dear Sir,         I, Kousik Kundu, am a Ph.D student at university of Freiburg,

Re: [PyMOL] Help Needed

From a purely structural perspective you can look at the interface residues script on the PyMOLWiki: http://pymolwiki.org/index.php/InterfaceResidues The interface could be detected by run /path/to/interfaceResidues.py fetch 1bm2 interfaceResidues 1bm2, c. A, c. L But, you

[PyMOL] help about mutation

I am querious to know on what mathematical basis does the software mutates the amino acids. -- Chandan kumar Choudhury NCL, Pune INDIA -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial.

Re: [PyMOL] help about mutation

: Wednesday, September 09, 2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] help about mutation I am querious to know on what mathematical basis does the software mutates the amino acids. -- Chandan kumar Choudhury NCL

Re: [PyMOL] help with removing script (using Vista 64-bit)

, 2009 3:40 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] help with removing script (using Vista 64-bit) Dear PyMOL users, When I first began using PyMOL, I accidentally installed a script as one might a plugin, obviously to no avail. Now whenever I start the program, I receive

[PyMOL] help with uninstall

Dear PyMOL users, When I first began using PyMOL, I accidentally installed a script as one might a plugin, obviously to no avail. Now whenever I start the program, I receive the following message: Exception in plugin 'color_by_attype' -- Traceback follows... Traceback (most recent call

[PyMOL] Help! from pymol import cmd pops up unwanted GUI

I am rather new to pymol. Now, I want to use it as a module withing a python script but importing the module brings up the GUI when I execute the script. See below the toy script: #!/usr/bin/python from pymol import cmd cmd.load('foo.pdb') This script, when executed in my machine, will pop up

[PyMOL] Help with APBS

Hi everybody, I need some help on getting APBS working on pymol. Tough I know you'll tell me to go to the wiki, I need somebody to help me because I just can't get it done following the instructions on the wiki. MAC OS X 10.5.2 and MacPymol 0.99rc6 running on a PPC G4 computer I have

[PyMOL] help with batch mode

Colleagues, Does anyone have a good method for generating alignment statistics in batch mode using pymol? I think I'd like to do something like: pymol -c sup.py data.txt where sup.py is something like: load ./final/final.001.pdb load ./final/final.002.pdb fit

Re: [PyMOL] help with batch mode

Hey Michael, with some commands, you can use the (somewhat poorly documented) option 'quiet=0' to get results sent to standard output, like so: load ./final/final.001.pdb load ./final/final.002.pdb fit (final.002///13-30/c,ca,n), (final.001///13-30/c,ca,n), quiet=0 Andreas Michael Summers

Re: [PyMOL] help with batch mode

-boun...@lists.sourceforge.net] On Behalf Of Michael Summers Sent: Wednesday, February 13, 2008 8:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] help with batch mode Colleagues, Does anyone have a good method for generating alignment statistics in batch mode using pymol

Re: [PyMOL] help with batch mode

[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Andreas Förster Sent: Wednesday, February 13, 2008 11:20 AM To: Michael Summers Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] help with batch mode Hey Michael, with some commands, you can use the (somewhat poorly

[PyMOL] Help on state and frame

Hello, I´m just starting with Pymol and having a task of making a movie. I tried to find the difference between state and frame but couldn´t. Please help, thanks alot! Send instant messages to your online friends http://uk.messenger.yahoo.com

[PyMOL] Help for X.org-based Stereo 3D on Linux?

PyMOL Users, We have gotten a couple of questions recently regarding running nVidia-based Stereo 3D under the X.org X-server instead of using XFree86. We don't have X.org set up in house yet, so I was hoping someone else might be able to provide a definitive answer as to whether or not it

[PyMOL] help!

Hi! I am getting the following error when I try to set stick transparency of my object ligand PyMOLset stick_transparency, ligand, 0.7 Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\setting.py, line 586, in set v = (float(value),) ValueError:

[PyMOL] Help with labels?

Hi, I am trying to add labels to my figures to get them ready for publication. I have figures in both stereo and mono, and I'm trying to figure out how to move/orient labels so that they are easy to view. Are there ways to move labels in a figure? cheers Jamie Wallen

[PyMOL] Help with labels?

Hi Jamie, I've attached an email from a response to a similar question posted awhile ago. I hope it is helpful. Ciao, Scott On Oct 18, 2004, at 8:07 AM, jwal...@csb.wfu.edu wrote: Hi, I am trying to add labels to my figures to get them ready for publication. I have figures in both stereo

Re: [PyMOL] Help with labels?

A little side note: Ray tracing in stereo should be done with: ray width, height, angle=-3 png image_right ray width, height, angle=3 png image_left instead of with turn y, -3 to the first script turn y, 3 to the second one in order to get the shadows right Andreas

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, Unfortunately, there is no CGO ellipsoid. What you might try is represent the units in the lattice as arrows as to indicate their orientation (determined as the principal or principle ;) axis), and have one unit in (cartoon) detail, with a more slender arrow inside. I think it

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, the easiest solution is probably to create a fake pdb file with dummy atoms (located roughly in the center of mass) to represent each molecule in your ASU. make sure the pdb file contains the same CRYST entry as your original file. you can load it into pymol and then scale up the

[PyMOL] Help/suggestions for illustrating lattice arrangement

Hi, I am trying to prepare a figure illustrating a fairly complex packing arrangement in a large H32 (R32) unit cell, where the packing may actually have some biological relevance. To try and show the packing I've been generating symmetry related molecules using the symexp command. The

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, * Roger Dodd rb...@cam.ac.uk [2004-10-07 16:33] wrote: I am trying to prepare a figure illustrating a fairly complex packing arrangement in a large H32 (R32) unit cell, where the packing may actually have some biological relevance. To try and show the packing I've been

Re: [PyMOL] help compiling/ running APBS plugin on macG5

I also notice that the same place that has APBS has this site that computes electrostatics from a PDB file and returns a PQR file. This would be lovely for people like me to use for the calculations. Now how can I use the PQR file to create an electrostatic surface with pymol? A PQR file

[PyMOL] Help for user-defined functions

Does anyone know if it is possible to add 'help' documentation to my own user-defined functions? What I want is to be able to define a new PyMOL command by executing the following script: #-- def some_func: ''' Some help docs here... ''' #

Re: [PyMOL] Help for user-defined functions

Hi, I haven't seen this documented anywhere, so I have no idea if it's the Right Way to do things, but I think all you need to do is add cmd.help_sc.append('some_func') after the cmd.extend('some_func',some_func) call. should this be built in to cmd.extend()? -michael -- This isn't a

Re: [PyMOL] HELP Load biological unit

Dear All, Help, I don't know what I am doing wrong. I want to load a dimer into pymol, 3GRS, the standard PDF file from the PDB bank only gives co-ordinates for a monomer but if I download the PDB file for the biological unit

[PyMOL] help regarding PyMol

I am doing a post-doc in south korea. I am interested in plotting molecular data in the form of 3-D animated pictures. My data has been generated by 3-D Molecular Dynamic code MOLDY. I have installed the Python and PyMol and run the sample problems. The input of Pymol is in PDB format,

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