Re: [PyMOL] creating a virus capsid using supercell.py

2015-04-17 Thread Ezra Peisach 
The full biological unit should be available in biological assembly file.
Have you tried using the fetch command?

i.e.:

fetch 1avd, type=pdb1

set all_states, on


The first retrieves BA #1, the all_states shows the models.

If there is something wrong with the assembly file - then by all means
contact the PDB...

Ezra



On Fri, Apr 17, 2015 at 1:34 AM, Marcelo Marcet  wrote:

> Hi Everyone,
>
> I have been trying to build a virus capsid using pymol. The biological
> unit for the complete structure is not available. :(
>
> My first attempt at getting this done was by using the “rotate” and
> “translate” commands. Unfortunately, these commands can only move objects
> either relative to the main axes or the viewer’s position (not relative to
> existing objects), thus I had to calculate the rotation angles and
> translation angle/distances for every single object (not practical).
>
> I have been advised to try the ‘supercell.py’ script. Is supercell the
> right tool for the job? Any advice would be much appreciated.
>
> Marcelo
>
>
>
>
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Re: [PyMOL] pdb edition

2016-01-19 Thread Ezra Peisach 
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 present.

On Tue, Jan 19, 2016 at 5:48 PM, David Hall  wrote:

> 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 mode
> http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move
>
> And then save http://pymolwiki.org/index.php/Save
>
>
> But honestly, the description sounds like something that would be
> infinitely easier to do using some plain python code rather than in pymol.
>
> -David
>
>
> On Jan 19, 2016, at 4:59 PM, Edward A. Berry  wrote:
>
>
>
> 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 aim?
>
> Cheers,
>
>
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate
> atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>
>
> Tsjerk
>
> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta   > wrote:
>
>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, breaking bonds and separating atoms.
>3. The third step will be to save the resulting structure as
> structure2.pdb file.
>
>I wonder if  pymol allows me to perform this task.  iI hope someone can
> guide me in this task.
>
>Thanks in advance
>
>Pascual
>=
>
>
>Pascual Lahuerta
>Universitat de Valencia
>Dep. Q. Inorganica
>Edificio Investigación 3.36
>Dr. Moliner 50
>46100 Burjassot-Valencia
>Despacho 96 354 3147
>Movil 617 188 331
>lahue...@uv.es 
>
>
>
>
>
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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

2016-02-22 Thread Ezra Peisach 
1hho does have a non-standard crystal frame. (see remark 285)

If you load the assembly PDB file in rasmol - it displays properly. Pymol
is having the issue.

However, if you fetch the cif file in pymol, and ask it to display the
assembly - it does the right thing.

set assembly, 1
fetch 1hho


Ezra

On Mon, Feb 22, 2016 at 5:04 AM, Spencer Bliven 
wrote:

> This looks like a bug in the PDB's file, and you should definitely let
> them know about it. It's a particularly weird case since the second model
> doesn't correspond to any of the valid crystallographic operators. Probably
> it is a problem with the very non-standard crystal frame specified by the
> SCALE matrix in the PDB file. These are always problematic, to the point
> that some tools (e.g. EPPIC ) will ignore them
> completely.
>
> While waiting for the PDB to fix the file, you can generate the biological
> unit from the symmetry operators using:
>
> fetch 1hho, async=0
> symexp sym, 1hho, 1hho, 2
>
> -Spencer
>
> On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns 
> wrote:
>
>> Dear Ioannis,
>>I was wondering about that, too.  Given the prominence of hemoglobin
>> structure and oxygen binding in Biochemistry education, the 1 HHO structure
>> seems to be a bad biological structure to calculate incorrectly.  I guess
>> an email to the PDB might be in order (if it is intentional, they could at
>> least explain it in that case).
>> Best Regards,
>>   Jim
>> 
>> From: Ioannis Michalopoulos 
>> Sent: Monday, February 22, 2016 4:05 PM
>> To: Jame R.Ketudat-Cairns
>> Subject: Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
>>
>> Dear Jim,
>>
>> Thank you for your prompt answer which worked perfectly. I was writing a
>> tutorial for my students and I found many incorrectly calculated
>> biological
>> units. I wonder if we should complain to PDB about it, or wait and see
>> what
>> PyMOL can do about it, first.
>>
>> Best Regards,
>>
>> Ioannis
>>
>> On Monday 22 of February 2016 02:09:05 you wrote:
>> > Dear Ioannis,
>> >The 1HHO biological unit seems to be calculated incorrectly (just
>> spun
>> > around the y-axis 180 degrees).  I found that the symexp command works
>> for
>> > this: symexp sym, 1hho, (1hho), 1
>> > Best Regards,
>> > Jim
>> > 
>> > From: Ioannis Michalopoulos 
>> > Sent: Monday, February 22, 2016 3:39 AM
>> > To: pymol-users@lists.sourceforge.net
>> > Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho]
>> >
>> > Dear PyMOL users,
>> >
>> > I run PyMOL 1.8.0.0 for Windows.
>> >
>> > I loaded the biological assembly of 1HHO:
>> >
>> > http://www.rcsb.org/pdb/files/1HHO.pdb1.gz
>> >
>> > When I tried:
>> >
>> > split_states 1hho
>> >
>> > PyMOL failed to produce the proper tetramer that is seen at:
>> >
>> >
>> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO&opt=3&bionumber=1
>> >
>> > Instead PyMOL shows a weird tetramer. Is it a bug? This approach works
>> > fine on other cases eg 1SVC. Is there any other way to do it?
>> >
>> > Thank you in advance.
>> >
>> > Best Regards,
>> >
>> > Ioannis
>> > --
>> > Dr Ioannis Michalopoulos
>> > Staff Research Scientist - Associate Professor Level
>> > Centre of Systems Biology
>> >
>> > Tel: +30 210 6597 127
>> > Fax: +30 210 6597 545
>> > Email: imicha...@bioacademy.gr
>> > _
>> > Biomedical Research Foundation, Academy of Athens
>> > Soranou tou Efessiou 4, 115 27 Athens, Greece
>> >
>> >
>> >
>> 
>> > -- Site24x7 APM Insight: Get Deep Visibility into Application
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>>
>> --
>> Dr Ioannis Michalopoulos
>> Staff Research Scientist - Associate Professor Level
>> Centre of Systems Biology
>>
>> Tel: +30 210 6597 127
>> Fax: +30 210 6597 545
>> Email: imicha...@bioacademy.gr
>> _
>> Biomedical Research Foundation, Academy of Athens
>> Soranou tou Efessiou 4, 115 27 Athens, Greece
>>
>>
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Re: [PyMOL] Support for Python 1.5.2?

2002-01-11 Thread ezra peisach 
As long as you update the external source package (and all
dependencies) to python 2, I have no objection. I feel that pymol is a
moving target and if you need the latest and greatest tools, use them.
My only concern is performance. If moving to python 2 has a
performance hit, then I would be concerned.

For my compilations, I treat pymol as a separate beast - which includes
python in it's own little tree - so a new version of python is no problem.

   Ezra

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

2016-11-28 Thread Ezra Peisach 
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...

Of course, there have been many different flavors of PDB files produced by 
different programs...

http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER

On 11/28/2016 10:31 AM, Spencer Bliven wrote:
> 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 mmCIF.
>
> On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder  > wrote:
>
> 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,
> > 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
> > fairly trivial problem to solve.
> >
> > Best regards,
> >
> > Rui
> >
> > Le 28/11/2016 10:41, Marko Sever a écrit :
> >> 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 position of atoms in the pdb file.
> Residues are ok but atoms in a given residue are mixed up. It also added
> addition TER's which I had to manually delete.
> >>
> >> So how would I specify the output PDB format to be the same as in the
> original imported pdbs (before manipulation), so same as CHARMM pdb 
> format.
> >>
> >> Please help,
> >>
> >> Marko
>
> --
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> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> 
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Re: [PyMOL] Problem with PDB file export

2020-01-21 Thread Ezra Peisach 
The dots and question marks are appropriate. You did not export a PDB 
file, but instead an mmCIF/PDBx file.


For an explanation of what the fields mean, you can look at 
http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html



On 1/21/20 9:46 PM, Ofir Shein Lumbroso wrote:

Hi all,
I'm a new user of PyMOL and I'm trying to export a PDB file from a 
PyMOL session and It seems to have some errors. I'm using the default 
settings and I'm getting some dots and question marks in the 
exported PDB file, can you please help?


I attached a corrupted PDB file for example.

Thanks!
Ofir

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