Re: [PyMOL] PDB post-processing and TER records

Awesome, thanks so much Jared for your usefull suggestions! all the best james вт, 25 июн. 2019 г. в 22:00, Jared Sampson : > > Hi James - Glad you got it working. > > > chains_array = ["A", "B"] > > If you want a list of chains without having to hard-code them, try the > `get_chains` command.

Re: [PyMOL] PDB post-processing and TER records

Hi James - Glad you got it working. > chains_array = ["A", "B"] If you want a list of chains without having to hard-code them, try the `get_chains` command. ``` chains_array = cmd.get_chains() ``` > cmd.load('${pdb}') > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"') Alternatively,

Re: [PyMOL] PDB post-processing and TER records

I have got it, it works now! in my example the double quotes were not escaped in pymol script :-) the only (more python-oriented) question, would it be possible to indicate chains_array for all letters A-Z (e.g. using some python regex, rather just for A and B, chains_array = ["A", "B"], like in m

Re: [PyMOL] PDB post-processing and TER records

I actually tried to do like that still defining chains_array = ["A", "B"] inside of pymol script and use external bash loop to loop over pdbs but it does not works ;( #!/bin/bash # this script rename chains in pdb to "empty" chain home=$(pwd) pdb_folder=$home/pdbs output=$home/output rm -r $output

Re: [PyMOL] PDB post-processing and TER records

yes, actually it is better because we avoid looping! and how it would be possible to use array provided in the externall shell? #!/bin/bash pdb="final.pdb" output=$(pwd) # array given in bash chains_array=('A' 'B') # chains are cutted by pymol pymol -c -d " cmd.load('${pdb}') cmd.alter('chain '

Re: [PyMOL] PDB post-processing and TER records

If you want to rename multiple chains at once, make a selection like (chain A+B+C). This list selection syntax is documented here: https://pymolwiki.org/index.php/Property_Selectors cmd.load(pdb) cmd.alter('chain ' + '+'.join(chains_array), 'chain=""') cmd.save('output.pdb') Cheers, Thomas

Re: [PyMOL] PDB post-processing and TER records

in python version I have got it # to be run with PyMOL: #pymol -ckqr pymol_cut_off.py cut_off.py # from pymol import cmd pdb = "final.pdb" chains_array = ["A", "B"] # two chains will be cuted for chain in chains_array: cmd.load(pdb) cmd.alter('chain ' + chain, 'chain=

Re: [PyMOL] PDB post-processing and TER records

OK Lorenzo, thank you ! As an alternative question, would it be possible to put that loop while renaming of the chains in the processed PBD within the bash loop? Here is an idea #!/bin/bash # this script rename chains in pdb to "empty" chain pdb="my.pdb" output=$(pwd) # chain array is provided

Re: [PyMOL] PDB post-processing and TER records

thanks so much Thomas, for this example! Actually, your python script does exactly what my bash script - produces number of pdbs for each of the renamed chain. I would like rather to produce at the end ONE pdb with all chains renamed to empty chain... I guess I need to save the result outside of t

Re: [PyMOL] PDB post-processing and TER records

Hi James, not sure if it's relevant in this case, but you might also want to use retain_order, to avoid messing up your pdbs. https://pymolwiki.org/index.php/Retain_order Cheers, Lorenzo Il giorno mar 25 giu 2019 alle ore 16:04 Thomas Holder < thomas.hol...@schrodinger.com> ha scritto: > > gene

Re: [PyMOL] PDB post-processing and TER records

> generally if I integrate a pymol silent script inside my > bash script, I do not need to use cmd.* syntax, right? Correct. The -d argument takes PyMOL commands, like a .pml script. Python syntax is optional. Python syntax (cmd.*) is necessary and most useful if you write a Python script (.py

Re: [PyMOL] PDB post-processing and TER records

one extra programming question: imagine now in my pdb I have severals chain which I would like to rename to blank chain. I can do it simply like this # a case for 3 chains to be renamed #!/bin/bash pdb="my.pdb" output=$(pwd) pymol -c -d " cmd.load('${pdb}') cmd.alter('(chain A)', 'chain=\"\"') c

Re: [PyMOL] PDB post-processing and TER records

Hi James, pdb_use_ter_records works in PyMOL 2.3.0, but not in previous versions (was broken and then removed). See https://pymolwiki.org/index.php/pdb_use_ter_records Cheers, Thomas > On Jun 25, 2019, at 10:25 AM, James Starlight wrote: > > Dear Pymol Users! > > I need to process input P

[PyMOL] PDB post-processing and TER records

Dear Pymol Users! I need to process input PDB via pymol (this time no need to do it via no-gui mode!!) to remove chain id from PDB. I am using alter command to do it with the following syntax #rename chain A to phantom chain :-) alter (chain A),chain='' the problem that in my initial PDBs there

Re: [PyMOL] PDB structure to .obj or .fbx

A short how-to https://www.macinchem.org/reviews/3D/augmented.php <https://www.macinchem.org/reviews/3D/augmented.php> Cheers Chris > > Message: 1 > Date: Fri, 31 Aug 2018 12:26:03 -0400 > From: Abel J Baerga Ortiz > To: pymol-users@lists.sourceforge.net > Subject:

[PyMOL] PDB structure to .obj or .fbx

Hello all, Is there any way to convert a .pdb structure to a .obj or .fbx file? I would like to incorporate protein structures into virtual reality experiences and these are the common formats. Abel Baerga Ortiz U of Puerto Rico -- Abel Baerga Ortiz, PhD. Catedrático Asociado Departamento de Bi

Re: [PyMOL] PDB Format not correct for use in CHARMM

PDB format dictates that TER records are present at the end of a polymer chain. Chain breaks or non-sequential numbering do not introduce TER records. A TER record is required between the polymer and non-polymer chain - even with same chain ID. TER records should not be between non-polymers...

Re: [PyMOL] PDB Format not correct for use in CHARMM

It would be nice to have a setting that adds TER records only where the chain or segi change (as opposed to whenever the residue numbers are non-sequential). I believe that better captures the original intent for terminating polymers. Of course, the real answer is that everyone should switch to mmC

Re: [PyMOL] PDB Format not correct for use in CHARMM

Hi Marko and Rui, The TER records can also be prevented with "set pdb_use_ter_records, off". https://pymolwiki.org/index.php/pdb_use_ter_records Cheers, Thomas On 28 Nov 2016, at 05:03, Rui Sousa wrote: > Hi Marko, > > For the order of the atoms, check if "retain_order" is set to 1; if not

Re: [PyMOL] PDB Format not correct for use in CHARMM

Hi Marko, For the order of the atoms, check if "retain_order" is set to 1; if not, use "set retain_order, 1" before importing your PDB file. For the rest of your problem, what exactly is being changed from the imported PDB file and the saved one? Apart from the addition of TER, which is a fair

[PyMOL] PDB Format not correct for use in CHARMM

Hello everybody, I'm working with a protein-protein complex and am fixing some stuff. When I save the fixed complex as a pdb the PDB format is not the same as it was in the imported pdb files (there it was the same as the CHARMM default pdb format). In the saved pdb it changed the line positio

Re: [PyMOL] pdb edition

Hi Edward, Oh, I read over the moving part. Well, what I meant to convey is that you can use CONECT records to draw additional bonds, but for the rest bondedness is inferred from distance. So you can only remove bonds if the particles are further apart than the cutoff AND have a CONECT record. Bu

Re: [PyMOL] pdb edition

Thanks, David! My take- Pymol is a very powerful tool for creating beautiful and insightful figures of molecules, with myriad features for displaying aspects of interest to structural biologists, such as different surfaces, electrostatic potential, H-bonds and other inter-atomic interactions, secon

Re: [PyMOL] pdb edition

CONECT records are not used for peptide bonds for standard amino acid and nucleic acid links. These are assumed. In addition, for these standard chemical component, CONECT records are not used to internal bonds - they are "known." Non standard amino/nucleic acids used CONECT records for all atoms

Re: [PyMOL] pdb edition

Well, yes, programs do use the CONECT records, including pymol http://pymolwiki.org/index.php/Connect_mode Removing bonds is http://pymolwiki.org/index.php/Unbond Atoms can be translated using the command line http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python Or in edit

Re: [PyMOL] pdb edition

On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote: > Hi Pascual, > > The PDB file does not really have information on bonds. If atoms are closer > than some cutoff a bond is drawn. Unbonding and saving will not change the > distance, so the bond will be drawn again when loaded again. What is your

Re: [PyMOL] pdb edition

Hi Pascual, The PDB file does not really have information on bonds. If atoms are closer than some cutoff a bond is drawn. Unbonding and saving will not change the distance, so the bond will be drawn again when loaded again. What is your aim? Cheers, Tsjerk On Tue, Jan 19, 2016 at 12:15 PM, Pasc

[PyMOL] pdb edition

I am new user of Pymol and I would like to use this program for a very simple task that I describe here in three steps: 1. Start with a simple structure (structure 1.pdb1) either loaded or created with the editor. 2. The second task will be to change the position of the atoms in structure 1,

Re: [PyMOL] .pdb files and rendering software

Hi again, Joe - Try saving in COLLADA format with `save myfile.dae` (in PyMOL v1.7.3.2 or later). If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because Blender only supports polylists for COLLADA import, and not the more effi

[PyMOL] .pdb files and rendering software

Hi all, I was wondering the best options for importing .pdb files into rendering programs like Maya or Blender. Right now I'm trying mMaya with Maya2014 but seem to have many issues. Any suggestions? Thanks, JoeG -- ___

Re: [PyMOL] pdb to string

Hi, > I want to dump a loaded pdb file to a string, the inverse of the function > read_pdbstr(). There is such a function available? cmd.get_pdbstr() will do the job. Best regards, Takanori Nakane -- LIMITED TIME SALE

Re: [PyMOL] pdb to string

Thanks a lot! Osvaldo. On Mon, Sep 16, 2013 at 8:01 PM, Takanori Nakane < t.nak...@mail.mfour.med.kyoto-u.ac.jp> wrote: > Hi, > > > I want to dump a loaded pdb file to a string, the inverse of the function > > read_pdbstr(). There is such a function available? > > cmd.get_pdbstr() will do the j

[PyMOL] pdb to string

Hi, I want to dump a loaded pdb file to a string, the inverse of the function read_pdbstr(). There is such a function available? Thanks in advance. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1

Re: [PyMOL] pdb of ice

hua +64 3 4797034 > > > -Original Message- > From: H. Adam Steinberg [mailto:a...@steinbergs.us] > Sent: Friday, 21 October 2011 9:31 a.m. > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pdb of ice > > Hi all, > > Does anyone know of

Re: [PyMOL] pdb of ice

...@steinbergs.us] Sent: Friday, 21 October 2011 9:31 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pdb of ice Hi all, Does anyone know of a pdb that was created for the structure of water molecules in ice? I have not been able to find one and am not looking forward to creating one! :) H

[PyMOL] pdb of ice

Hi all, Does anyone know of a pdb that was created for the structure of water molecules in ice? I have not been able to find one and am not looking forward to creating one! :) H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366

Re: [PyMOL] PDB: How to extract

Hi Sergey, > How to extract only two beads within 7? I have two beads with big > bond distance between them and i want to obtain their id's in original > pdb file. PyMOL's internal bond cutoff is much smaller than your 70,000 Ang. You will need to use the cutoff parameter if you're using dis

[PyMOL] PDB: How to extract

How to extract only two beads within 7? I have two beads with big bond distance between them and i want to obtain their id's in original pdb file. -- Kind regards, Sergey Ivanov -- Benefiting from Server Virtualizati

Re: [PyMOL] pdb-l: chain alignment tool

Inside a script, I would suggest adding ",async=0" so that the fetch command is forced to complete before the next command is read: fetch 1a25, async=0 show cartoon create chaina, chain a ... ... -- Subject: Re: [PyMOL] pdb-l: chain alignment tool Hi, There are many. One way is to

Re: [PyMOL] pdb-l: chain alignment tool

Hi, There are many. One way is to use PyMol (or, indeed many other viewers). So I did it like this: fetch 1a25 show cartoon create chaina, chain a create chainb, chain b delete 1a25 align chaina, chainb color red, chain a color blue, chain b I guess that this could be generalised into a script t

Re: [PyMOL] PDB changed CONNECT records

ists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Thursday, September 06, 2007 11:24 AM To: 'Mark A Saper'; 'Pymol' Subject: Re: [PyMOL] PDB changed CONNECT records Mark, set connect_mode = 0 is the default, and this uses

Re: [PyMOL] PDB changed CONNECT records

alf Of Mark A Saper Sent: Thursday, September 06, 2007 10:48 AM To: Pymol Subject: [PyMOL] PDB changed CONNECT records This was previously discussed in an archived email but I can't find it right now. Does the setting connect_mode=0 use the CONECT records in the PDB file or not? I think it

Re: [PyMOL] PDB changed CONNECT records

AFAIK setting connect_mode=1 strictly uses the CONECT records from pdb file to draw bonds. Cheers, Abhi. On 9/6/07, Mark A Saper wrote: > > This was previously discussed in an archived email but I can't find it > right now. Does the setting connect_mode=0 use the CONECT records in the > PDB f

[PyMOL] PDB changed CONNECT records

This was previously discussed in an archived email but I can't find it right now. Does the setting connect_mode=0 use the CONECT records in the PDB file or not? I think it does. Apparently in pdb code 1ABE, the CONECT records were changed in a 2005 revision. Two alternate sugar conformat

Re: [PyMOL] PDB loader

'surendra negi'; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PDB loader > > Hi All, > > Yes indeed, the PDB has broken PyMOL's PDB loading > capabilities (the 'fetch' > command and the PDB Loader plugin) by eliminating the old URL download > interface

Re: [PyMOL] PDB loader

Nice, I just fixed this problem by pointing to my local PDB archive (i.e. http://www.bmrb.wisc.edu/servlet_data/pdb/pdb1brv.ent) but The Developer fix works great too of course! -- Jurgen F. Doreleijers, Ph.D. BMRB, Univ. of Wisconsin-Madison, WI, USA mailto:jurge...@gmail.com

Re: [PyMOL] PDB loader

Here are five lines using wget in perl #how to use: perl a.pl [pdbfile 4 letter code] #perl a.pl 1dn2 $pdbn=$ARGV[0]; $pdbn=~ tr/a-z/A-Z/; $temp = sprintf "-q -O %s.pdb \"http:\/\/www.rcsb.org\/pdb\/files\/%s.pdb\?format=PDB&pdbId=%s&compression=None\

Re: [PyMOL] PDB loader

ginal Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of surendra negi > Sent: Wednesday, October 18, 2006 8:00 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] PDB loader > > Hi, > In pymol, PDB

Re: [PyMOL] pdb

New PDB file location is http://www.rcsb.org/pdb/files/$pdbfilename.pdb.gz http://www.rcsb.org/pdb/cgi/export.cgi/$pdbfilename.pdb is not working sn __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo

Re: [PyMOL] PDB loader

heers, Jerome Pansanel Le mercredi 18 octobre 2006 16:59, surendra negi a écrit : > Hi, > In pymol, PDB loader service is no longer working. My > > self downloader script is also not working! They > changed > the file location. There is no more export.cgi in pdb > web site. > sn

[PyMOL] PDB loader

Hi, In pymol, PDB loader service is no longer working. My self downloader script is also not working! They changed the file location. There is no more export.cgi in pdb web site. sn __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best

Re: [PyMOL] pdb files with many chains

Hi Siv, Try giving each chain a unique identifier. As pymol might believe that all the fragments belong to chain ' '. Cheers Noel On Wednesday 23 August 2006 22:40, Siv Midtun Hollup wrote: > Hi, > > Hope this is the correct place for this question :) > > I have a pdb file with many small fr

[PyMOL] pdb files with many chains

Hi, Hope this is the correct place for this question :) I have a pdb file with many small fragments in addition to a longer chain. These are not numerated in any way, only separated by TER (example below). In pymol, only two 'chains' appear, one with the long chain, and the other with all the fra

[PyMOL] PDB center

Dear User, Is it possible to change center of the coordinate system in pymol to (0,0,0). I want to change center of my PDB file to orgin. thanks surendra __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.

[PyMOL] PDB and Windows XP

Dear users, While trying to read relatively large PDB files with PyMOL 0.98 I get runtime errors under Windows XP and the program terminates. It used to work better under PyMOL 0.97 and Windows 2000. Small files seem to be OK. Does anybody know a solution to this? Thanks, Leonid Sazanov

RE: [PyMOL] PDB parse error?

On Fri, April 8, 2005 12:19 pm, Warren DeLano said: > Gareth, > > Looking over the code, we're using sscanf for most of the PDB field > reads...so there's no way around this short of changing the source code > and > recompiling. However, are spaces legal within PDB field entries? They > would be

RE: [PyMOL] PDB parse error?

50)-346-1154 > . mailto:war...@delsci.com > > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > > Gareth Stockwell > > Sent: Friday, April 08, 2005 6

RE: [PyMOL] PDB parse error?

areth Stockwell > Sent: Friday, April 08, 2005 6:25 AM > To: pymol-users > Subject: [PyMOL] PDB parse error? > > > Warren, > > Using version 0.97, if I load a PDB with an atom like this: > > HETATM 2051 N A HEM B 400 -7.209 4.751 30.974 1.00 > 16.78

[PyMOL] PDB parse error?

Warren, Using version 0.97, if I load a PDB with an atom like this: HETATM 2051 N A HEM B 400 -7.209 4.751 30.974 1.00 16.78 N (e.g. in PDB 1f1c) Then Pymol loads the atom name as 'N' rather than 'N A'. Is there a way around this? Gareth -- Gareth Stockwell European B

[PyMOL] pdb loader service

hello, is it possible to use the pdb loader in a *.pml style script? thanks, marc

Re: [PyMOL] PDB to DXF

A quick Google for "pdb dxf" suggests that there are a couple: http://www.okino.com/conv/imp_pdb.htm http://www.danforthcenter.org/smith/MolView/Writeup/file.htm ... although this article http://www.sciencemag.org/cgi/content/full/281/5384/1814a suggests that MolView's DXF output is poor. hth, G

[PyMOL] PDB to DXF

Hi, Is it possible to convert a .pdb in a .dxf (AUTOCAD) file? Does anyone know how? Thanks in advance, andre ambrosio PhD student cbme/ifsc/usp - brazil

RE: [PyMOL] PDB Insertion code (iCode) treatment by PyMol

; Sent: Tuesday, March 09, 2004 7:23 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] PDB Insertion code (iCode) treatment by PyMol > > Hello, > I would like to know how PyMol treats the residues with an > insertion code from a PDB file. > How can I select the

[PyMOL] PDB Insertion code (iCode) treatment by PyMol

Hello, I would like to know how PyMol treats the residues with an insertion code from a PDB file. How can I select the residues with an insertion code (for example 324a)? How can I color them? Thank You. Ilya

Re: [PyMOL] PDB SS Question

> They are different, especially at the ends of the helixes ... the web SS > seems to have longer helixes than the pdb HELIX info. Is one more > 'correct' than the other? If in doubt, obtain DSSP (it might be installed locally already) and go with whatever it tells you: http://www.cmbi.kun.nl/gv/

[PyMOL] PDB SS Question

Following question concerns Secondary Structure of hemoglobin pdb 1BZ0 If the PDB comes with HELIX information do I still need to add the secondary structure from the web (http://www.mbfys.lu.se/Services/SecStr/)? They are different, especially at the ends of the helixes ... the web SS seems to h