Re: [PyMOL] secondary structure disappears

Big thank you to all of you! I really need to find some time to better learn code. :/ > On Jul 23, 2015, at 4:36 PM, Sampson, Jared wrote: > > I'm posting the following solution on behalf of Thomas Holder (whose > sourceforge.net email address is currently down due

Re: [PyMOL] secondary structure disappears

I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.net email address is currently down due to SF server issues), to ensure it is added to this thread in the archive: This is due to chain identifier conflict. He's merging 6 models with identic

Re: [PyMOL] secondary structure disappears

Hi Adam, I think you also want to make sure that each strand as a distinct chain ID if you want the cartoon representation to work correctly. Unfortunately that means you have to use "alter" but to change the chain IDs on the objects created by the split_states command before merging them all int

Re: [PyMOL] secondary structure disappears

Hi Adam, You can use iterate to get the secondary structure designation, and then use alter to apply it to the other chains. secstruc=[] iterate model1 and n. ca, secstruc.append(ss) s1=list(secstruc) alter model2 and n. ca, ss=s1.pop(0) The last two lines need to be repeated, including the cop

Re: [PyMOL] secondary structure disappears

I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones. Smith At 2015-07-23 22:23:24, "H. Adam Steinberg" wrote: Hi All, If you fetch 3ow9 in PyMOL, split_states to get all six of the strands,

Re: [PyMOL] secondary structure disappears

The secondary structure is only there for the first set of strands, and then that is used for the other strands when you split_states, but how do I change that entry so it applies to the other strands? Here is that entry from the file that I attached: SHEET1 A 2 LEU A 2 PHE A 5 0

[PyMOL] secondary structure disappears

Hi All,If you fetch 3ow9 in PyMOL,split_states to get all six of the strands,select all, then copy to object,You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.If I open the pdb file for 3ow9 in text edit and remove all the

Re: [PyMOL] Secondary structure for C-alpha only and coarse-grained models

Thanks a lot Tsjerk, It iw really going to be helpful. I will update you when I play with it. best, Abhi On Sat, Nov 9, 2013 at 12:46 PM, Tsjerk Wassenaar wrote: > > Hey :) > > I thought there was a post recently about showing secondary structure in > C-alpha only models. I can't find it anym

[PyMOL] Secondary structure for C-alpha only and coarse-grained models

Hey :) I thought there was a post recently about showing secondary structure in C-alpha only models. I can't find it anymore, but in any case it's something popping up now and again. For reconstruction of high-resolution models out of coarse-grained ones, I came up with a very simple algorithm for

Re: [PyMOL] Secondary structure labeling

Hi Bishwa, what you want is to label one representative atom per secondary structure element. So figure out chain and residue number of those atoms, and label each of them individually: PyMOL> label A/42/CA, "beta1" PyMOL> label A/117/CA, "alpha1" PyMOL> label A/147/CA, "alpha2" For changing lab

Re: [PyMOL] Secondary structure labeling

Hi Bishwa, can you be more precise what you mean by "label"? If the secondary structure is defined in the header of your PDB file, PyMOL can show cartoon representation, show text labels on C-alpha atoms and color by secondary structure. PyMOL> as cartoon PyMOL> label name CA, ss PyMOL> color red

Re: [PyMOL] Secondary structure labeling

Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bish

Re: [PyMOL] Secondary structure motifs

Hi James, The 2D representation of secondary structures you show, is not possible with PyMOL. You would need to extract the secondary and code up the solution yourself. I bet there are servers out there that will do this for you, Cheers, -- Jason On Sun, Nov 20, 2011 at 11:20 AM, James Starligh

Re: [PyMOL] Secondary Structure Element from a PDB file

Hi Anna, On Sat, Aug 20, 2011 at 2:30 AM, Anna James wrote: > > Is there any program/code/software which can give me the secondary structure > region in a given PDB file ? > > like : > ./ executable pdb1.pdb > answer would be : > > alpha helical : 1- 8 residues > beta sheet : 17-29 residues > et

Re: [PyMOL] Secondary Structure Element from a PDB file

Thanks Robert Can you please give out some examples on how to use them? Please give out some appropriate links for stride and dssp Thanks again! Best Anna From: robert.fenw...@irbbarcelona.org Date: Sat, 20 Aug 2011 08:49:56 +0200 Subject: Re: [PyMOL] Secondary Structure Element from a PDB

[PyMOL] Secondary Structure Element from a PDB file

Is there any program/code/software which can give me the secondary structure region in a given PDB file ? like : ./ executable pdb1.pdb answer would be : alpha helical : 1- 8 residues beta sheet: 17-29 residues etc... so on OR can this be done in Pymol ,I tried using dss but I gues

Re: [PyMOL] Secondary structure bug?

Matthias Schmidt wrote, On 06/28/11 13:37: > I am making a movie in pymol that I prepared with g_morph > > g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4) > > Pymol does not assign the secondary structure. > > load movie.pdb > dss, movie PyMOL calculates the consensus seco

[PyMOL] Secondary structure bug?

Hi I am making a movie in pymol that I prepared with g_morph g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4) Pymol does not assign the secondary structure. load movie.pdb dss, movie assigns incorrect secondary structure. In my case, dss models a complete transmembrane hel

Re: [PyMOL] Secondary Structure Matching

c [mailto:fke...@ulg.ac.be] > Sent: Wednesday, October 21, 2009 5:51 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Secondary Structure Matching > > Hello, > > Is there a way to perform secondary structure matching with > Pymol. I already tried the align

Re: [PyMOL] Secondary Structure Matching

I normally use this command with that purpose: align obj1&(ss h)&name ca, obj2&(ss h)&name ca That is, obj2 is structurally aligned onto obj1 on the basis the CA trace on the regions where secondary structure matches alfa helix (ss h) Hugo Kerff Frédéric wrote: > Hello, > > Is there a way to per

[PyMOL] Secondary Structure Matching

Hello, Is there a way to perform secondary structure matching with Pymol. I already tried the align function with different selections without any success but the 2 proteins obviously share the same fold with low sequence identity. I know it can be done in other software like Coot but I'd like to

[PyMOL] Secondary structure elements

-->> Message: 2 >> Date: Fri, 28 Nov 2008 16:39:19 +0300 >> From: DimitryASuplatov >> Subject: [PyMOL] Secondary structure elements >> To: pymol-users@lists.sourceforge.net >> Message-ID: <1227879559.914.24.ca...@leiden.genebee.msu.ru> >> Content-Ty

Re: [PyMOL] Secondary structure elements

Hello, Possibly. I have python code that attempts to parse dssp files. Add that to a script to call dssp (not so hard) and then call the parsing code, then annotate the structure with the result... Maybe all this already exists somewhere? gilleain On Fri, Nov 28, 2008 at 1:39 PM, DimitryASupla

[PyMOL] Secondary structure elements

Hello, Is there a way to incorporate dssp into pymol for secondary structure annotation? Thank you. SDA

Re: [PyMOL] Secondary structure coloring

there is set cartoon_highlight_color, command to set the highlight color to grey or something, so you can use that to color the other side of the secondary structure. On 10/10/07, Omar Davulcu wrote: > > Hi everyone, > > I've noticed that in some PDB files, not all, when I attempt to color a >

[PyMOL] Secondary structure coloring

Hi everyone, I've noticed that in some PDB files, not all, when I attempt to color a piece of secondary structure, like a helix, only one side will be colored and the underside is grey. I've even noticed that if I load two different PDB files in the same session, one will color both sides and

Re: [PyMOL] secondary structure to different states

Hi Björn, Odd. I can't reproduce this. I load 1a2p and 1a12 into states one and two, hide, show cartoon, and bingo - I have two cartoons (in two different states). What happens if you load the first pdbfile twice? Or use another file instead of p2? Or a newer version (I'm using MacPyMol 1.0.0b03

[PyMOL] secondary structure to different states

Hi all, If I read in a two pdb-files in different states, only the first one read in got assigned secondary structures. Example: load p1.pdb ,state=1 load p2.pdb ,state=2 hide all show cartoon only p1 has arrows and helixes the p2 has fat tubes. I also tried define it explicitly

Re: [PyMOL] secondary structure

Hi Karen, There sure is a way to fix this. Use the following statements: alter 96-103/, ss='S' alter 96-103/, ss='H' alter 96-103/, ss='L' to set residues 96-103 to beta Strand, alpha Helix, and Loop respectively. You can asssign your whole sequence this way from the Procheck assignments. Good

[PyMOL] secondary structure

Hi Everyone, PyMol is incorrectly assigning a couple of residues in my structure as loop region where it should really be a beta strand (according to procheck). I was wondering if there was any way to change this so I can see the strand in the cartoon rendering? I am also having the same

[PyMOL] Secondary structure and surface

Greetings PyMolers: I have a couple of questions. I am working on some figures and have found, at least for my particular protein, the DSS in PyMol does a better job with secondary structure assignments than DSSP. I have checked the assignments against the map and model in O. Is there any

[PyMOL] Secondary Structure assignments and Molscript compatability

Hello All, I am a long-time Molscript user and devotee and am trying to make the move to PyMol for various reasons. A lot of the structures I work with are at moderate-low resolution making automated secondary-structure prediction difficult and most of them don't contain SS flags in the origin

RE: [PyMOL] secondary structure and movie

rren 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.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of

RE: [PyMOL] secondary structure assignment and surface potential calc/mapping

ist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Neiditch, Matthew > Sent: Friday, October 31, 2003 12:46 PM >

[PyMOL] secondary structure assignment and surface potential calc/mapping

Dear List, 1) Is the secondary structure assignment function in 0.92 more reliable? Or does the "WARNING: it will make mistakes, so don't publish anything based on this algorithm!" statement still apply? 2) Is there a 0.92 function to calculate and map surface potential? This would be useful be

RE: [PyMOL] secondary structure and movie

rom: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Alan Wilter Sousa da Silva > Sent: Friday, October 31, 2003 3:48 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] secondary structure and movie > > > Hi List! >

[PyMOL] secondary structure and movie

Hi List! I did a polyalanine in helix ss. I tested: 1: dss (ok) 2: run stride_ss.py, stride2pymol (ok) 3: dssp (from rtools) (???) Case (1) differs a little bit from (2) in N term. Case (3) seems not to work. Or, maybe, I do not know how to use it. Tried via menu and via command dssp. Got the s

[PyMOL] Secondary structure for superposed structures

Hi, I'm a very new pymol user so bear with me if I've missed something obvious. I want to get nice cartoon representations of superposed structures - I obtained the rTools (from http://www.rubor.de/bioinf/pymol_rubor.html) as was mentioned previously on the mail-list and this is working fine

Re: [PyMOL] secondary structure colouring

Dear Laurence This is actaully in the FAQ http://pymol.sourceforge.net/faq.html#SECCOLOR Daniel +-+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: d

[PyMOL] secondary structure colouring

Can anyone help me with the selection commands in PyMOL to select (and subsequently colour) residues by their secondary structure ? Many Thanks, Laurence -- --- Laurence H. Pearl Section of Structural Biology, Institut

[PyMOL] Secondary Structure, DSSP etc

Hi, I currently have an implementation of DSSP in C++ with lots of improvements such as correctly identifying Pi-helices. The output of the program is pseudo-PDB, so you could paste it to the top of your PDB file and most programs, including PyMol would read it accurately. The output additional

Re: [PyMOL] Secondary structure assignments

I've got a crude interface to the RasMol code which lets you run RasMol's secondary structure assignment code from PyMOL at: http://www.rahul.net/pcm/rasmolapi.tar.gz I don't make any promises as to how well it works or whether I will ever get around to cleaning up the ugly code. If there are

Re: [PyMOL] Secondary structure assignments

On Tue, 20 Aug 2002, Peter C. McCluskey wrote: > >The other thing I'd find useful is some molecular mechanics tools, > >particularly energy minimization. Blending PyMOL with MMTK seems like a > >good way to do this, since MMTK's license looks fairly liberal. I think we're all of the same mind on

Re: [PyMOL] Secondary structure assignments

dee...@iastate.edu (dee...@iastate.edu) writes: >On Mon, Jul 29, 2002 at 01:12:40PM -0400, Nathaniel Echols wrote: > >> How hard would it be to incorporate the DSSP algorithm? I was looking at >> the source for RasMol, which has a complete implementation. My feeling is >> that this could be port

Re: [PyMOL] Secondary structure assignments

> The best way to avoid "derivative work" concern is to code in a "clean room" > fashion, without reference to someone else's code. In principle, this could > be done working from the original paper(s) that describe an algorithm. I assume this is what authors of other packages have done in the pa

Re: [PyMOL] Secondary structure assignments

On Mon, Jul 29, 2002 at 01:12:40PM -0400, Nathaniel Echols wrote: > How hard would it be to incorporate the DSSP algorithm? I was looking at > the source for RasMol, which has a complete implementation. My feeling is > that this could be ported without too much misery. However, RasMol's > licen

Re: [PyMOL] secondary structure again

I made a mistake giving the URL in my last post, the correct DSSP page is now http://www.cmbi.kun.nl/gv/dssp/index.html Sorry for this. Virgile ADAM

Re: [PyMOL] secondary structure again

Dear Marco, you can find DSSP at http://www.embl-heidelberg.de/dssp/ or could prefer use Procheck from the CCP4 series (http://www.ccp4.ac.uk/) and run it on your pdb file by the "procheck [pdbfile] [chain number] [resolution]" command. You will obtain 10 postscript files in which you can find draw

[PyMOL] secondary structure again

I have a problem to load secondary structure. I read the previous mail and I do not have DSSP. Any other way to load the secondary structure information into pymol? thank you marco

Re: [PyMOL] Secondary structure assignments

OK, heres what we've got: The DSSP program is available for Linux and Windows from http://www.cmbi.kun.nl/swift/dssp/ . I have written a Python script that parses the output of DSSP and alters the annotation in PyMOL. You just start the script, then You have a dssp command available. The s

Re: [PyMOL] Secondary structure assignments

> Ideally util.ss could become a shell that would know (from the environment?) > if dssp or similar was installed, then either run dssp and parse the output > to assign the ss, or else run the ss asignment code in the current util.ss if > no other options were available. I've basically done thi

Re: [PyMOL] Secondary structure assignments

Nat, You read my mind. Having just converted the output of DSSP manually to PDB records last week I was eyeing the source to util.ss wondering how to turn it into a dssp parser. Ideally util.ss could become a shell that would know (from the environment?) if dssp or similar was installed, th

Re: [PyMOL] Secondary structure assignments

> Yes, please. There are some structures that have to be generated by using > symmetry operations defined in the "REMARK 350" lines in the pdb file > (example: > 1jjy.pdb). The only way (I know of, if you know a better one, please tell me) > to > do this is going to http://pqs.ebi.ac.uk where the

Re: [PyMOL] Secondary structure assignments

Le Sun, 28 July 2002, Nathaniel Echols a écrit > but I'm working on making it more general. I suppose since I only use > this for loading files into PyMOL, I could just write it in Python as a > PyMOL module. . . would that be useful to anyone else? Yes, please. There are some structures that h

Re: [PyMOL] Secondary structure assignments

Le Sun, 28 July 2002, Nathaniel Echols a écrit > but I'm working on making it more general. I suppose since I only use > this for loading files into PyMOL, I could just write it in Python as a > PyMOL module. . . would that be useful to anyone else? Yes, please. There are some structures that h

Re: [PyMOL] Secondary structure assignments

> programs. So I am in search of a solution. Can one manually create a > secondary structure assignment matrix to insert into the PDB file? I must > admit that as a novice I do not understand the formatting of the secondary > structure matrices that I have seen embedded in some PDB files. Is t

[PyMOL] Secondary structure assignments

Dear Pymol users, I am very pleased with Pymol as a visualization tool for the generation of publication quality images, but I am having a problem with one aspect of the problem. I am working with several PDB files that do not have embedded secondary structure assignments. I have been trying to

[PyMOL] secondary structure headings in .ent files

Hello All, I have the following problem. Whenever I attempt to load a pdb file from the RCSB (eg- a .ent file), I get the following error. ObjectMolecule: read HELIX A 231 A 241 ObjectMolecule: read HELIX A 265 A 286 ObjectMolecule: read HELIX A 293 A 317 ObjectMolecule: read HELIX A 334 A 3

RE: [PyMOL] secondary structure

> How does this affect movies involving conformation changes? Secondary > structure info from the first frame appears to carry over > into the others- > whereas in reality some helixes or sheets change to varying > degrees. This > leads to warping in something like calmodulin. Would I need to

Re: [PyMOL] secondary structure

> You can bypass the requirement for having secondary structure in the PDB > file by explicitly assigning secondary structure using the alter command. Ah. This is probably what I was looking for. > PyMOL just stores one bit of secondary structure information per residue > (the "ss" property of

Re: [PyMOL] secondary structure

On Tue, 12 Feb 2002, Nat wrote: > > Forgive my ignorance, but what would be the best way to add secondary > structure data to a PDB file, or coerce it into some format that PyMOL can > read? I've been fiddling around with STRIDE and DSSP, but the outputs > from these need to be parsed into the o

[PyMOL] secondary structure

Forgive my ignorance, but what would be the best way to add secondary structure data to a PDB file, or coerce it into some format that PyMOL can read? I've been fiddling around with STRIDE and DSSP, but the outputs from these need to be parsed into the official PDB format for secondary structure a

RE: [PyMOL] secondary structure and many more questions

That's the spirit Jason -- don't hold back with those questions! > From: Jason Yano [mailto:jky...@bragg.bio.uci.edu] > 1) Is there a way to find out what secondary strucuture has been > assigned by the automatic algorythem? > I assume there must be a python command that will dump the > output

[PyMOL] secondary structure and many more questions

Hello All, I had a few questions: 1) Is there a way to find out what secondary strucuture has been assigned by the automatic algorythem? I assume there must be a python command that will dump the output of the utility to the screen or to a file. 2) Is there any information available for a