[PyMOL] Question on geometry option in replace command

Dear users, Could I ask a question on geometry option in replace command? I tried to use Build/Fragment/XXX to replace an atom to a new one, and pymol GUI shows the corresponding replace command. However, I found the geometry option always equals to 4. For example, PyMOL>replace O, 4, 2 PyMOL>repl

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

Hi Martin, There are currently no plans to migrate Timeline to open source. Best, Jarrett J. On Mon, Jan 20, 2025 at 1:49 PM Martin Urban wrote: > Hi Jarrett, > > thanks for the quick reply. This is a good thing to know, perhaps it > should be stated more clearly on the wiki page. Are there an

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

Hi Martin, Timeline and its corresponding Python API is only available for on Incentive versions. Jarrett J. On Mon, Jan 20, 2025 at 1:42 PM Martin Urban wrote: > Dear PyMOL Community, > > I am exploring the Timeline Python API as described on the PyMOL Wiki ( > Timeline Python API

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

Hi Jarrett, thanks for the quick reply. This is a good thing to know, perhaps it should be stated more clearly on the wiki page. Are there any plans for it to be open source one day? Best regards, Martin On 20.01.2025 19:44, Jarrett Johnson wrote: Hi Martin, Timeline and its corresponding

[PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

Dear PyMOL Community, I am exploring the Timeline Python API as described on the PyMOL Wiki (TimelinePythonAPI ). However, when I attempt to use |timeline_add_composition()|, I encounter the following error: /AttributeError: module 'pymol

[PyMOL] Question about rotation in latest version of Pymol

Hello, I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to do that by using the command: “rotate axis, angle, selection”. But any axis that I use, gives out very long bonds that look definitely wrong. Except for doing it manually, (using command key+ left click) are

Re: [PyMOL] Question on residue selection in multiple PDB

Thank you so much Jarrett, yes it works very well! On Thu, 20 Jul 2023 at 08:51, Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Sorry, typo. For the second approach, state should be `i + 1` and not `-1`" > > Jarrett J. > > On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson < > jarrett.j

Re: [PyMOL] Question on residue selection in multiple PDB

Sorry, typo. For the second approach, state should be `i + 1` and not `-1`" Jarrett J. On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Neena, > > Is the split_states necessary? You can query the distance between atoms on > the state-level as well wi

Re: [PyMOL] Question on residue selection in multiple PDB

Hi Neena, Is the split_states necessary? You can query the distance between atoms on the state-level as well without having to break up your structure. Here's two approaches that show either way; I recommend the second if possible. You'll of course have to switch out the selection string to fit yo

Re: [PyMOL] Question on residue selection in multiple PDB

Hello PyMOL users, Can I get some insight on how to approach this analysis? Many thanks, Neena On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen wrote: > Hello PyMOL Team, > > I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 > NMR structures deposited in it. > Using spli

[PyMOL] Question on residue selection in multiple PDB

Hello PyMOL Team, I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 NMR structures deposited in it. Using split_states command, I can see all 38 structures. I want to find polar contacts between same 3 residues in all these 38 structures and extract corresponding distance v

[PyMOL] Question about formatting font size

Dear Users, I found in pymol layout somehow characters including protein sequence letters become very small. Not sure what I have done. Any ideas of changing to a bigger font? Thanks a lot in advance! Kind regards, Chao ___ PyMOL-users mailing list Arch

[PyMOL] Question regarding transparency

Dear Pymol users, I have a question about transparency. I would like to transparent both the cartoon and the surface to highlight the sticks, but when I transparent both of them, the cartoon will disappear, how do you solve this? Thank you in advance!

Re: [PyMOL] Question about glm in pymol

300 Fenglin Road, Shanghai, 20032, P.R.China > Tel: 86 21 5492 4218 > Fax: 86 21 5492 4015 > Email: mhzh...@sippe.ac.cn > > > *From:* Jarrett Johnson > *Date:* 2022-07-13 00:33 > *To:* 张敏华 > *CC:* pymol-users > *Subject:* Re: [PyMOL] Question about glm in pymol > Hello

Re: [PyMOL] Question about glm in pymol

Hello, Through CentOS, you should be able to install glm with yum package manager. yum install glm-devel More info can be found here: https://pymolwiki.org/index.php/Linux_Install . Also take note that if you're using Centos 7, the default glm may not have a modern enough API for PyMOL code. I

Re: [PyMOL] Question about glm in pymol

2-07-13 00:33 To: 张敏华 CC: pymol-users Subject: Re: [PyMOL] Question about glm in pymol Hello, Through CentOS, you should be able to install glm with yum package manager. yum install glm-devel More info can be found here: https://pymolwiki.org/index.php/Linux_Install . Also take note that if yo

[PyMOL] Question about glm in pymol

Dear all: I want to comple open-source-pymol in CentOS. So I want to using the latest glm. So how to install glm? or I just put the glm folder into the include folder in the open-sourde-pymol folder? Minhua Zhang, Ph.D., Assistant Professor Structural Biology Lab Institute of Plant Ph

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

Hi Jeff, That would be cmd.disable("object name") # https://pymolwiki.org/index.php/Disable Cheers, Ali On 1/3/21, 9:05 pm, "Jeff Saxon" wrote: Thank you very much, Ali! Yes, actually, I suppose I have set up vdw radii using those commands, considering specific selections,e.g

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

Thank you very much, Ali! Yes, actually, I suppose I have set up vdw radii using those commands, considering specific selections,e.g this is part of my pymol script that I am using in bash. $pymol -c -d " from pymol import cmd cmd.load('${storage}/${syst_name}/all_clusters.pdb') cmd.split_states('

[PyMOL] Question: Align object from group (and move rest of group with it)

Dear all, I am trying to align (or pair fit) two structures and, at the same time, move a density map belonging to the mobile structure with the alignment. What would be the best way to achieve that? I'd appreciate help or suggestions! Thanks in advance! Best, Jacek __

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

Hi Jeff, The sphere size is controlled by the vdw property, to change it: alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon you also need to use the "rebuild" command to implement the changes At this point, you can contro

[PyMOL] Question about python command in PyMOL

Hello, My name is Vik, I'm writing a python script that allows a user to input a TSV (tab-separated value) file of PDB's which then edits them. I'm now trying to change the code so that it can run directly in PyMOL instead of having to run this python script and PyMOL separately. I'm having troubl

[PyMOL] Question about multi-sequence edition in PyMOL

Hi, I have a question regarding adding peptide sequence to the original sequence in PyMOL. I have an original structure of a nanoparticle consisting of 420 monomers and I like to add a similar peptide sequence to each monomer. Is that any easy way to apply a sequence addition/ change to one monome

Re: [PyMOL] Question about python commands in PyMOL

y 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.edu.au From: Ali Kusay Date: Thursday, 2 July 2020 at 8:55 pm To: Ali Kusay Subject: FW: [PyMOL] Question about python commands in P

[PyMOL] Question about python commands in PyMOL

Hello, I'm writing a python script that loads in PDBs then selects certain chains colors them according to a standardized chart. However, I've run into the issue where my when I try running my script in Pymol via the run command it just displays the text on the python script but doesn't actually e

[PyMOL] Question: How can I analyze the binding strength/energy between a small molecule and DNA using Pymol?

Dear PyMOL maillist people: I am new to mail lists. Please excuse any breaks of convention. I suspect that a small molecule I am working with may have some DNA binding property due to its triphenylphosphonium group. I would like to assess this using Pymol. How could I do this? I do not have much ba

Re: [PyMOL] Question about Pymol method / ESP rendering

Hi Thomas, Thank you for your reply. I made the cube file by using psi4 which is one of quantum chemistry package. I will check the file. Kind regards, Taka 2019年6月11日(火) 19:40 Thomas Holder : > Hi Taka, > > Your ESP.cube file doesn't look like an electrostatic potential map, it > looks like ele

Re: [PyMOL] Question about Pymol method / ESP rendering

Hi Taka, Your ESP.cube file doesn't look like an electrostatic potential map, it looks like electron density. You need two map files, one for the density, and one for the ESP. Cheers, Thomas > On Jun 8, 2019, at 12:39 AM, Taka Seri wrote: > > Dear Pymol users, > I am newbie of Pymol. > I h

[PyMOL] Question about polymer selection criteria

Hello, I have a question about how the pymol polymer.nucleic selection defines what is nucleic? Is there a list of atom names that are required? Does it have to actually be part of a polymer for the selection process to identify it? If someone can help me understand this, that would be great. Tha

[PyMOL] Question about pymol movies

Hi Pymol Users, I need your help with an issue related to movie in pymol. I know how to change the representation of the molecule that appears in my movie at a given frame but I don't find the way to change the representation of just a given part of such molecule, lets say make some residues becom

Re: [PyMOL] PyMol Question

Mohsen– set transparency , .5, sele Cheers, Spencer On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi there, > > > > I was wondering how I can make the surface of a selected part of a protein > transparent?

[PyMOL] PyMol Question

Hi there, I was wondering how I can make the surface of a selected part of a protein transparent? I tried transparency command, but, I came up with a message that "transparency" was not found. Thank you -- _

Re: [PyMOL] Question regarding scene states

Sorry, I found the answer to my own question. madd 1 -10 If you don't use xframes, then it won't add additional frames to single-state objects. I can't quite figure out the rationale for that but if you already have pre-loaded states before you use mset, you can't request additional frames.

[PyMOL] Question regarding scene states

Hi List, I figured out a hack way to fix my last question. That's ok, because I have another one. In my movie I have some objects with multiple states, and some objects with one. Is there a way to use mset (or in my case madd) for the multiple state objects and disregard the other objects? For

Re: [PyMOL] question about biological units, states, etc.

Hi Dave, You can set the chain identifier for each object alter object, chain="A" And then you can create a new object create alltogether, chain A+B+C+D That object you can then use for fitting. Hope it helps, Tsjerk On Wed, Oct 3, 2012 at 7:22 PM, Bourgaize David wrote: > Hello, all. > >

Re: [PyMOL] question about biological units, states, etc.

Hi, Look into the "create" command - this should allow you to create a new object from multiple starting objects/selections. Pete Bourgaize David wrote: > Hello, all. > > First let me announce that I am not a PyMOL poweruser, and I have virtually > no experience with crystallography and its d

[PyMOL] question about biological units, states, etc.

Hello, all. First let me announce that I am not a PyMOL poweruser, and I have virtually no experience with crystallography and its data files. I have been plugging along using the PyMOLwiki as my knowledge-base for years, but cannot seem to wrap my head around certain issues. For example, 6pfk

Re: [PyMOL] Question about mutagenesis wizard

Hi. I tried a little: *test1.pml* # See http://www.pymolwiki.org/index.php/Peptide_Sequence # See http://www.pymolwiki.org/index.php/propka reinitialize cd C:\Users\tlinnet\Desktop python for aa in "CVGLTSW": cmd._alt(string.lower(aa)) python end create pdb1, cys remove cys delete cys save

Re: [PyMOL] question

Was my message received by the pymol group about combining camera and object motions at the same time? It said it was held for review. I have "copy myself" on the mailman server, but I never seem to receive my own posting. Jordan On Sep 19, 2012, at 5:35 AM, Thomas Holder wrote: > Hi Mona, >

Re: [PyMOL] question

Hi Mona, > I am very interested to here if it is possible to align a stick > structure with a cartoon strucrture in Pymol? structure alignment is independent of visual representation. So yes, you can align a "stick structure" to a "cartoon structure". > Is it possible to put the short aa code or

[PyMOL] question

hi Jason I am currently using pymol and I have I question about 3D cartoon > structures: > I am very interested to here if it is possible to align a stick structure > with a cartoon strucrture in Pymol? > Is it possible to put the short aa code or name in the peptide structure in > pymol? sincerel

Re: [PyMOL] Question about mutagenesis wizard

Hi Thomas, thank you for your response. Actually, the modeling part comes later in the process. First, I need to perform this step in pymol. In fact, it would facilitate the modeling process. Sincerely, -- Maurício M Rigo 2012/9/14 Thomas Holder > Hi Maurício, > > what you describe here i

Re: [PyMOL] Question about mutagenesis wizard

Hi Maurício, what you describe here is called homology modeling. Although PyMOL has some modeling capabilities, I'd strongly recommend to use a real homology modeling tool such as MODELLER to do this. http://salilab.org/modeller/ Hope that helps. Cheers, Thomas Maurício Menegatti Rigo wro

Re: [PyMOL] Question about mutagenesis wizard

Dear Pymol users, > > I'm a begginer with command lines in Pymol. I'm trying to complete the > following task through a pymol script: > > 1) Write a file named "file1.txt" with an aminoacid sequence (e.g. CVGLTUW) > > 2) Open a .pdb molecule (file2.pdb) with the same number of residues, but >

Re: [PyMOL] Question about ray tracing, set_view, surface smoothness

Hi Gudrun, Gudrun Lotze wrote: > Dear all, > > I wish to ray trace my object so it looks nice. I have chosen a mesh as > surface representation. > > I did > viewport 1024, 768 > ray 1024, 768 > > But the mesh is black afterwards and not anymore blue. > Is there a chance to keep the color and hav

Re: [PyMOL] Question about ray tracing, set_view, surface smoothness

Hi Gudrun, > But the mesh is black afterwards and not anymore blue. You may want to check your light position, or try a slighter blue. > Is there a chance to keep the color and have less dominant lines for the mesh? I'm not artistically skilled enough to know about less dominant lines, but the

[PyMOL] Question about ray tracing, set_view, surface smoothness

Dear all, I wish to ray trace my object so it looks nice. I have chosen a mesh as surface representation. I did viewport 1024, 768 ray 1024, 768 But the mesh is black afterwards and not anymore blue. Is there a chance to keep the color and have less dominant lines for the mesh? Is there a cha

[PyMOL] Question

Dear All, I am a Pymol's user I would like to know how could I find the algorithm publication of three functions for superimposition of multi-structures? 1- fit 2- align 3- super I would thanks in advance for your reply Sincerely B. Ch On Wed, Feb 15, 2012 at 12:20 PM, Bachar Cheaib wrote:

Re: [PyMOL] Question Iterate

Hi Martin, The temporary namespace for an atom means that variables like 'resn' can be used to refer to the attribute with that name on the atom instance. You are right that iterate is here used to iterate over a single atom. That does seem a bit odd :p But it seems to be a more straightforward w

[PyMOL] Question Iterate

In this example below (from Thomas), the method 'iterate' is used. The function saves every amino acid of a structure to a separate file. First of all, I'm not sure of how to understand the docs: " "iterate" iterates over an expression within a temporary namespace for each atom." What does tem

Re: [PyMOL] Question about the .obj file saved by Pymol

Hi Francois, Woops--sorry for the delay. I think only the outside vertices are sent. To get the inside, try set surface_cavity_mode, 2 before surfacing and exporting. You can also set that to '3' to include pockets as well as cavities. Cheers, -- Jason On Wed, Mar 2, 2011 at 3:04 AM, Franc

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

[PyMOL] Question about the .obj file saved by Pymol

Hello, If I use "save myscene.obj" and I was looking at the surface representation of a molecule, does the file contains only the external surface of the protein, or are the internal cavities also included? Thanks, F.

Re: [PyMOL] Question about Iterate and Edit-Mode

Hi Martin, You could think of it as what Tsjerk purported: # pseudocode for iterate def iterate(sel,cmd): for x in selection: return cmd(x) where each 'function' cmd would return a value per atom. For example, # pseucode for an instance of iterate def iterate(organic, 'print b') for

[PyMOL] Question about Iterate and Edit-Mode

Dear All I am trying to get behind the way 'iterate' works, since I see it quite frequently in PyMOL scripts. The example in the help page is a bit limited in the sense that I cant explain to myself what actually is happening. Say, if I were to write the functionality of 'iterate' using a for-lo

Re: [PyMOL] Question on how to identify residue number on protein surface

Hi Jay Song, Why not use code that's already available? Check out http://pymolwiki.org/index.php/FindSurfaceResidues. Cheers, -- Jason 2010/7/12 SongJianHui : > Hi all, > > I am trying using PyMol to identify the residue numbers on a protein > surface. I have been thinking use a low efficient

Re: [PyMOL] Question about ray

ananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea   +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > -Original Message- > From: Gudrun Lotze [mailto:gudrun.lo...@gmx.net] > Sent: Wednesday, 23 June 2010 12:30 p.m. > To: pymol

Re: [PyMOL] Question about ray

[mailto:gudrun.lo...@gmx.net] Sent: Wednesday, 23 June 2010 12:30 p.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Question about ray Dear Pymol-Users, I tried to ray my protein to get a good looking picture. I tried set ray_trace_mode, 0 and ray 1200, 1200. I always go a square around

[PyMOL] Question about ray

Dear Pymol-Users, I tried to ray my protein to get a good looking picture. I tried set ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my protein and parts where not visible. How can I get rid of that black border line and how can I ray my protein so it is on the whole page

Re: [PyMOL] Thank you for answering my pymol question! -one more question

er: alter original,chain="A" alter copied,chain="B" save dimer.pdb Cheers, Tsjerk On Wed, Apr 7, 2010 at 1:34 AM, JiangJiang Liu wrote: > Dear Tsherk : >     Thank you so much for your reply on my pymol question. Your suggestions > are helpful to solve the questio

[PyMOL] Thank you for answering my pymol question! -one more question

Dear Tsherk : Thank you so much for your reply on my pymol question. Your suggestions are helpful to solve the question that has been confused me for so long. I still have another related question. After I created the dimmer structure, do you know how to save the new structure as a pdb

Re: [PyMOL] Question about measuring volume

Hi Sing, You have a few options. You can try CASTp (either the web service or the PyMOL plugin). I think the .pocinfo file contains information about volumes. You could also use Voidoo (http://xray.bmc.uu.se/usf/voidoo_man.html). In the distribution, there is a script (cavity.csh) can be used

[PyMOL] Question about measuring volume

Dear all, I am wondering if it is possible for me to measure the volume of the binding pocket or the molecule in pymol? If no, any recommend program for Mac for such purposes? Thank you very much Sing -- This SF.Net

Re: [PyMOL] pymol question

Hi, You can draw a CGO circle in the yz plane using: x1,y1,z1 = -0.1, 0, 0 # start point r1,g1,b1 = 1,0,0 # color (red) x2,y2,z2 = 0.1, 0, 0 # end point r2,g2,b2 = 1,1,0 # color (yellow) radius = 10 cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" ) To m

Re: [PyMOL] pymol question

I'm sure there's a way to actually draw a circle, but for your particular use it might be better to use a sphere. If you're comfortable with python scripting, you can use CGO objects. If not, you might do something like this: fetch 1hhp create thing, resi 24 and name ca # create a new object from

[PyMOL] pymol question

Does anyone know how to draw a circle with a given radius in pymol? I have a distance that I want to use to see what residues lie on the end of that radius, but I have no idea how to write the command to draw the circle. Could someone help me please? ---

Re: [PyMOL] Question about Pymol movie

nal Message- > From: liyang [mailto:liy...@moon.ibp.ac.cn] > Sent: Monday, March 02, 2009 9:49 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Question about Pymol movie > > Dear all, >I got two small molecule binded protein structures, during > the reactio

[PyMOL] Question about Pymol movie

Dear all, I got two small molecule binded protein structures, during the reaction, this molecule moves from one site to another. Given the two pdb files, can I make a movie to simulate the whole process in Pymol? Any suggestion will be appreciated. -- Open WebMail Project (http://openwebmail.

Re: [PyMOL] another odd PyMOL question....

Subject: RE: [PyMOL] another odd PyMOL question Tom, label all, color will display the numeric color identifiers which can be used in place of color names. You can also use "iterate" to fetch them back out as a list: stored.list = [] iterate all, stored.list.append(color) print s

Re: [PyMOL] another odd PyMOL question....

ntific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Thomas Stout [mailto:tst...@exelixis.com] Sent: Tuesday, November 11, 2008 3:35 PM To: pymol-users@lists.sourceforge.net; matthew.frank...@imclone.com Subject: Re: [PyMOL] another odd PyMOL question So

Re: [PyMOL] another odd PyMOL question....

Subject: Re: [PyMOL] another odd PyMOL question "Thomas Stout" wrote on 11/11/2008 04:46:38 PM: > > Hi again everyone -- > > I have another odd PyMOL question: does anyone know if it is possible > to make selections based on what color certain atoms are? > I

Re: [PyMOL] another odd PyMOL question....

"Thomas Stout" wrote on 11/11/2008 04:46:38 PM: > > Hi again everyone -- > > I have another odd PyMOL question: does anyone know if it is > possible to make selections based on what color certain atoms are? > I need to do some wholesale re-coloring of a series of

[PyMOL] another odd PyMOL question....

Hi again everyone -- I have another odd PyMOL question: does anyone know if it is possible to make selections based on what color certain atoms are? I need to do some wholesale re-coloring of a series of complicated figures and it would be extremely useful if I could just say something like

Re: [PyMOL] question about checking the performance of PyMOL

Dear Warren Thank you for your information. It works fine. Joonghyun -Original Message- From: DeLano Scientific [mailto:del...@delsci.info] Sent: Sunday, October 26, 2008 3:25 AM To: 'Joonghyun Ryu'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] question about ch

Re: [PyMOL] question about checking the performance of PyMOL

Original Message- From: Joonghyun Ryu [mailto:jh...@voronoi.hanyang.ac.kr] Sent: Friday, October 24, 2008 10:39 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] question about checking the performance of PyMOL Hi, all I am sending this email for asking you about checking the per

[PyMOL] question about checking the performance of PyMOL

Hi, all I am sending this email for asking you about checking the performance of PyMOL. I tried to check the elapsed time for the computation of a molecular surface as follows. -- import os import cmd import pymol cmd.set("surface_quality", "2") start = time.time() cmd.show("surface") end = tim

Re: [PyMOL] question on making movie between two scenes with differentpoint of view

From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of liu junjun Sent: Monday, June 23, 2008 9:55 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] question on making movie between two scenes with differentpoint of view Hello everybody,

[PyMOL] question on making movie between two scenes with different point of view

Hello everybody, I'm trying to make a movie for chaning the point of view on a structure. I let PyMol read in matrix then define it as a scene. After the movie was set up, I can watch the movie playing well on the PyMol window. However, if I try to save the PNG sequence, I get few discontinuous pi

Re: [PyMOL] Question about PyMOL development

y, June 23, 2008 9:31 AM To: 'NeO'; 'supp...@delsci.com'; 'pymol-users@lists.sourceforge.net' Subject: RE: [PyMOL] Question about PyMOL development Fengyuan, Unfortunately, the PyMOL's internal gui pop-up menu system was not designed as nor intended to be a programmer

Re: [PyMOL] Question about PyMOL development

e.net Subject: Re: [PyMOL] Question about PyMOL development Hi Warren, I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've pre-defined all the cases that button actions and popup menu changes in function ' ExecutiveClick ', I can understand

Re: [PyMOL] Question about PyMOL development

Hi Warren, I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've pre-defined all the cases that button actions and popup menu changes in function ' ExecutiveClick ', I can understand only part of it. Now, I'm wondering that if I want to implement my thought ( - left-click the C

Re: [PyMOL] Question about PyMOL development

Dear Warren, How are you? I'm writing a wizard, in which I want to implement the function that when I left-click the C-alpha atom, there will be a PopUp window coming out with my defined information in the Viewer window. I can do it using 'tkMessageBox.showinfo', but I want to make it beautiful.

Re: [PyMOL] question about SUPER

Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jianghai Zhu Sent: Thursday, June 05, 2008 8:26 AM To: pymol-users Subject: [PyMOL] question about SUPER Hi, I am using SUPER to superimpose different structures in PyMOL. And

[PyMOL] question about SUPER

Hi, I am using SUPER to superimpose different structures in PyMOL. And I noticed that when I try to superimpose a lot of different structures onto one reference structure, the number of aligned atoms is getting smaller and smaller as I keep using SUPER command. And eventually structures

[PyMOL] FW: Pymol question

> I have a quick question for you. > I am trying to look at the structure of the tetranucleosome (pdb file 1zbb). > However, the structure is only composed by 2 nucleosomes. Is there a way to duplicate the image to 4? Based on the BIOMT records in the PDB file: REMARK 350 BIOMOLECULE: 1 REMARK

Re: [PyMOL] Question about electron density map (2)

Hi Adiphol, > electron density map. First, I only have .mtz file at a hand so could > anyone suggest me how can I convert this .mtz-file to the map or any file > that support to PyMol. Second, this is quite not so involve with the PyMol > program - sorry, if I would like to have an electron densit

[PyMOL] Question about electron density map (2)

Dear all, Thank you to Dr. Robert for my last question. However, I still have two more questions. I'm really lack of experience using PyMol to handle the electron density map. First, I only have .mtz file at a hand so could anyone suggest me how can I convert this .mtz-file to the map or any f

Re: [PyMOL] Question about electron density map with mtz file

Hi Adiphol * adi di [2007-05-11 10:26] wrote: > Dear all, > > I am trying to put on the electron density. I only > have .mtz file but I have a look at the manual and the > program need XPLOR file. How can I get the XPLOR file > or do I need to convert the mtz file to this - if so > how can I do

[PyMOL] Question about electron density map with mtz file

Dear all, I am trying to put on the electron density. I only have .mtz file but I have a look at the manual and the program need XPLOR file. How can I get the XPLOR file or do I need to convert the mtz file to this - if so how can I do that? Thank you very much Best Regards Adiphol

Re: [PyMOL] question on "state"

Will, The easiest approach, short of Python programming, is to temporarily load a new pdb file with updated coordinates and simply update the existing object before deleting the original. load original.pdb unset auto_zoom # then repeat the following as often as necessary set suspend_updates loa

Re: [PyMOL] question on "state"

Hi David, The state sort of refers to the frame or model in case of a multiframe/multimodel (multistate) system. You don't need to use it with set, it's optional. Just note that "dash_length" and dash_length are quite different things. Best, Tsjerk On 3/28/07, David Shin wrote: This regards

[PyMOL] question on "state"

This regards to my last post. I finally got it with: PyMOL>set dash_length, 0.1, measure01, 1 and got the message: Setting: dash_length set to 0.1 in object "measure01", state 1. but was wondering what "state" actually refers too... ie. previously, I tried: PyMOL>set "dash_length", 0.1, mea

[PyMOL] question about domain movement

Hi, I have built two models from one protein molecule with the different nucleotides bound: one is ATP, one is ADP. Their overall structures are similar except that a few secondary structure domains shift. For example, alpha4 helix has move left for about 1.2Å and rotate about 4º. Could I use pymo

Re: [PyMOL] PyMol question?

Hi, You can do this using alter_state: alter_state 1,selection,(x,y,z) = (a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2, a31*x+a32*y+a33*z+d3) where a11-a33 are the matrix elements (check whether they have to be transposed) and d1-d3 are the elements of the shift vector. It may

Re: [PyMOL] PyMol question?

The easiest way I'm aware of to do this would be to use the ccp4 program pdbset, but there are numerous other ways/programs that will do this (if pymol has this capacity, I'm not aware of it; but someone else will correct me). Pete >> I've been looking through the PyMol reference and wiki page

Re: [PyMOL] PyMol question?

Hi Mark: Most likely there is, but I don't know the answer to your question. I'm posting this to the pymol users list (via cc) so hopefully someone else will know the answer. I trust all is going well for you. Bill On Jun 30, 2006, at 8:19 AM, Mark Collins wrote: Hi Bill, I've been lo

Re: [PyMOL] Question on rotation

Hi Tsjerk > "Tsjerk" == Tsjerk Wassenaar writes: Tsjerk> There's a bit more to it. In the pymol view, the camera is located Tsjerk> at the origin, so to rotate your coordinates you first have to move Tsjerk> the center to the origin, do the rotation and move the thing Tsjerk> back. I've scrip

Re: [PyMOL] Question on rotation

Hi Terry, There's a bit more to it. In the pymol view, the camera is located at the origin, so to rotate your coordinates you first have to move the center to the origin, do the rotation and move the thing back. I've scripted this in Povray. If you're interested, I can send you the script. You can

[PyMOL] Question on rotation

I wrote a pymol plugin that produces a bunch of cgo. The images I generate have a cube drawn around them. I've been asked if it's possible to allow the user to initially rotate the image to their heart's content and then have the plugin draw the surrounding cube. I.e., once the image is rotated, t

Re: [PyMOL] Question about how to replace the amino acid

Adi, I have forwarded you some previous discussions on mutations. You will find your answer below. If you need anything further, please let me know. Best of Luck! Cheers, Nick --- Hi, I would like to ask how to change (modify or replace) th

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