Re: [PyMOL] Question on geometry option in replace command

Dear Lei, the best way to build a new molecule is via the builder in the GUI. The commands "replace" or "attach" are not well documented. I could reproduce your problem and I think PyMOL runs some kind of check routine after you issue a replace or attach command and it will reset the atomic

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

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

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

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('

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

Re: [PyMOL] Question about python commands in PyMOL

Hi Hrutvik, The print function doesn’t actually execute the PyMOL commands the “cmd” module does Change the prints to: cmd.load(“1u8q.pdb”) cmd.color(“red”,”chain y”) For specific instruction on how to use the cmd based functions, visit the PyMOL wiki Two other things: 1. the color functi

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

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.

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

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

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

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

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

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

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

Hi all, Joel's correct: to get the ray traced image to match the viewport, you must set the viewport to the same aspect ratio as the output image: # setup the viewport viewport 800, 600 # zoom on the visible zoom visible # ray the scene ray 800,600 # scale it up ray 1600, 1200 Cheers, -- Jas

Re: [PyMOL] Question about ray

Try setting your Pymol viewer to square dimensions first: Viewport 600,600 Then try the ray command This should work Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zeala

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

Re: [PyMOL] Question about Pymol movie

Liyang, This will only be of use to you if you happen to be a PyMOL subscriber, but there is an example movie script somewhat like this in the official online documentation: http://delsci.info/dsc/dokuwiki/doku.php?id=example:animation:granzyme_h ydrolysis Cheers, Warren > -Original Message

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

Joonghyun, To optimize performance and responsiveness, PyMOL tends to defer compute-intensive tasks until their results are actually needed. Thus, cmd.show("surface") Doesn't actually show a surface, it only sets the surface visibility flag on the atoms present (for future reference). An act

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

Junjun, What version are you using? Your script should work out of the box with the very latest PyMOL builds and open-source code. Prior to release 1.1, movies and scenes didn't work together so well because of timing issues (use of wall clock versus frame/movie clock). Those issues are finally

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

Jianghai, That sounds like a bug, but it could be something specific about your script. Could you post (or email us) an example PyMOL script which reproduces the reported behavior? Thanks! Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Mess

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

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

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

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

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

Re: [PyMOL] question about ca trace

4, 2006 4:29 AM Subject: Re: [PyMOL] question about ca trace Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol just traces through all c-alphas in the object, regardless of chains or distances. So, selecting the linked residues and hiding the trace should

Re: [PyMOL] question about ca trace

Tsjerk, Nice point, and probably easier to just create new objects in Pymol. nick - Original Message - From: Tsjerk Wassenaar To: pymol-users@lists.sourceforge.net Sent: Friday, April 14, 2006 4:29 AM Subject: Re: [PyMOL] question about ca trace Hi Tiger, Nick

RE: [PyMOL] question about ca trace

enaar > Sent: Friday, April 14, 2006 5:04 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] question about ca trace > > Hi Tiger, > > Nick is largely right. The cause for the link to show up is > that pymol just traces through all c-alphas in the object, >

Re: [PyMOL] question about ca trace

Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol just traces through all c-alphas in the object, regardless of chains or distances. So, selecting the linked residues and hiding the trace should solve your problem. Also, creating two files will do the trick. Alternat

Re: [PyMOL] question about ca trace

Tiger, I am no expert by far, but can you select the linkage? If so, just select and hide. Also, you might try just hiding the two residues that are linked, this might get rid of the link and you probably wouldn't notice the missing residues unless it is a small protein. alternatively, and

Re: [PyMOL] Question about custom CGO objects

Hi, As I understand it, you can either make cgo's that are 'static' in shape (like a 3D stamp) or use pymol.callback objects, which can use arbitrary opengl commands (such as matrix rotations). I actually made a cone, in response to someone's query, only I had to use callbacks to get tria

Re: [PyMOL] question about ray after alter and rebuild

Hi Pete, Check on the sections "clipped_by" and "bounded_by" in the povray documentation. You can clip with a defined plane, and can actually do so using different planes for different objects. Alternatively you can use other objects to clip. Another possibility is to use CSG difference or interse

Re: [PyMOL] question about ray after alter and rebuild

> Or you can dump to povray and render at whatever resolution you want, > but the image will not resemble exactly what is seen in the pymol viewer > window. > I've noticed problems with the clipping planes (z axis) whenever I've tried this. Specifically, the near clipping plane is apparently not

Re: [PyMOL] question about ray after alter and rebuild

Or you can dump to povray and render at whatever resolution you want, but the image will not resemble exactly what is seen in the pymol viewer window. Peter Adrian Meyer wrote: >>multiple structura alignment. I pointed out three structures for further >>processing within all 12 structures. However

Re: [PyMOL] question about ray after alter and rebuild

> multiple structura alignment. I pointed out three structures for further > processing within all 12 structures. However, when I try to ray the > structural > resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, > 2000', I > always received a low resolution (as screen resolution o

Re: [PyMOL] question about ray after alter and rebuild

--- Chung-Ming Yu wrote: > Dear all: > > I changed the topology of secondary structures with > 'alter' commands and then > I used 'rebuild' command to show the new topology of > secondary structures in > multiple structura alignment. I pointed out three > structures for further > processing wit

[PyMOL] Re： RE: [PyMOL] question about _cmd.pyd

I see. thank you for your answer. and i'm wondering, how do u develop python modules like _cmd.pyd? only via setup.py, and type python setup.py build to compile it? how do u debug it on the procudure of development? for me, it's not easy to develop _cmd.pyd only via setup.py script, i think, the

RE: [PyMOL] question about _cmd.pyd

Wen, The only form of end-user PyMOL compilation we support on Windows is via Python's distutils facility. Assuming that your system paths are set up correctly, distutils compilations will work fine with msvc6 -- no Makefile is required. Your own c/c++ code should be built as a standalone

Re: [PyMOL] question on cctbx and pymol

Hi, * Jianghai Zhu [2005-08-24 01:59] wrote: > > I could not get cctbx work under either MacPymol or PymolX11Hybrid in > Mac OS X. Anywhere I can find some instructions to get cctbx work in > OS X? There is a page on the cctbx with special instructions for using it on the Mac: http://cc

Re: [PyMOL] question on cctbx and pymol

Hi, I could not get cctbx work under either MacPymol or PymolX11Hybrid in Mac OS X. Anywhere I can find some instructions to get cctbx work in OS X? Thanks. Jianghai On Aug 23, 2005, at 1:18 PM, Sabuj Pattanayek wrote: Hi, This worked. Thanks, ..Sabuj Robert Campbell wrote: prefixing

Re: [PyMOL] question on cctbx and pymol

Hi, This worked. Thanks, ..Sabuj Robert Campbell wrote: prefixing a directory path. If you were like me and had: /usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the abo

Re: [PyMOL] question on cctbx and pymol

Hi Sabuj, * Sabuj Pattanayek [2005-08-22 18:03] wrote: > Hi, > > Thank you for replying. > > In fact this is what I did. Gentoo automatically compiles pymol (pymol > ebuild) with all required dependencies against the system-wide > python-2.4.1. I then manually installed cctbx, did "source >

Re: [PyMOL] question on cctbx and pymol

Hi, Thank you for replying. In fact this is what I did. Gentoo automatically compiles pymol (pymol ebuild) with all required dependencies against the system-wide python-2.4.1. I then manually installed cctbx, did "source /usr/lib64/python-2.4/site-packages/setpaths_all.csh" and "source /usr/

Re: [PyMOL] question on cctbx and pymol

Hi, * Sabuj Pattanayek [2005-08-18 16:08] wrote: > Actually I was wondering the same thing, except how to set it up in > linux. I was able to compile the cctbx but I'm not sure how to get it to > show up as a python module so that Pymol scripts (e.g. Dr. Campbell's > draw_cell.py) can work. An

Re: [PyMOL] question on cctbx and pymol

> I am trying some of pymol scripts from Prof. Robert L. Campbell, which require cctbx module. but I don't know how to put pymol and cctbx togther. > I download window version of cctbx/python2.4 bundle. and I download pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I got > an e

Re: [PyMOL] question on cctbx and pymol

Actually I was wondering the same thing, except how to set it up in linux. I was able to compile the cctbx but I'm not sure how to get it to show up as a python module so that Pymol scripts (e.g. Dr. Campbell's draw_cell.py) can work. Any help would be greatly appreciated. Yi Zhang wrote: Dea

Re: [PyMOL] question about selecting multiple residues

On Tue, 2005-03-22 at 14:09 -0500, Qun Wan wrote: > Hi, everyone: > If I want to select every cystein residues in my molecules, I think this works: select cysteins, resn Cys Kind Regards, ./ Kristoffer

Re: [PyMOL] question abut loading xplor map

On Fri, 14 Jan 2005 11:53:00 -0500, Qun Wan wrote: Hi, everyone: I have a simple question about loading the electron density map. I have generated x-plor format map and try to load it into pymol. However, pymol only shows me the unit cell, not the map. Does anyone know how can I "see" the map,

RE: [PyMOL] question about superposition

Qun, This is something that is easist to do with the Fitting wizard. Starting with the ATP, click successive matched pairs of atoms in the ATP and then the ADP. When you have enouch pairs, click Fit. That should be all you need to do. Cheers, Warren -- mailto:war...@delsci.com Warren

RE: [PyMOL] Question about surface calculation

Fred, I think Lieven answered the second part, so I'll answer the first: PyMOL's surfaces are discrete approximations of the solvent contact surface (the surface of waters in contact with the protein at all possible positions). I generally think of the "solvent accessible surface" as being the

Re: [PyMOL] Question about surface calculation

On Sunday 14 March 2004 06:27, Fred Berkovitch wrote: > When I type "show surface", how is that surface calculated? Is it a true > solvent-accessible surface? Does PyMol take into account heteroatoms > (e.g., a metal or an Fe-S cluster) in the calculation? As for the latter question, this is det

Re: [PyMOL] question on differential coloring of protein chains

On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins

Re: [PyMOL] question on differential coloring of protein chains

Hi Alex. > hello- > i am new to pymol and am trying to figure out how to differentially > color different chains (i.e. different proteins) in the structure i am > viewing. the structure i am working with is actually a structure of two > proteins that were co-crystalized and i would like assign d

RE: [PyMOL] Question

Avram, set cartoon_highlight_color, red Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.ne

RE: [PyMOL] Question

Hi Avram This is possible in cartoon mode in the newer versions of PyMOL (i don't remember exactly from which). You have to select "highlight color" in the cartoon menu. The default color is grey, but can be changed by set cartoon_highlight_color, , Cheers, Esben -Original Message--

RE: [PyMOL] Question on Mutagenesis

Rainbow, It's pretty simple: After activating the mutagenesis wizard, (1) CTRL-middle click on a residue of interest in your protein, (2) select the new residue type in the blue pop-up menu, (3) use the arrow keys to toggle through conformations, and then (4) click the apply button. Ch

RE: [PyMOL] Question about crystallographic symmetry

Hi Michael You seem to be after the biological assembly; in theory, pdb files from the PDB are supposed to have the matrix that will generate this somewhere in the header (REMARKS lines), and that shouldn't be too hard to parse out and apply explicitly to the molecule. Of course, pdb files are n

Re: [PyMOL] Question on clipping with surfaces

On Wed, 4 Sep 2002, Timothy Moore wrote: > I don't know whether this has been covered before but I have some > questions on clipping whilst using surfaces. Before I go on I will state > that pymol produces the best surfaces for my purposes, of any program I > have seen so far. However, (sorry ther