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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> 
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Re: [PyMOL] PDB Format not correct for use in CHARMM

2016-11-28 Thread Spencer Bliven 
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 <
thomas.hol...@schrodinger.com> 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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> 
> --
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Re: [PyMOL] PDB Format not correct for use in CHARMM

2016-11-28 Thread Thomas Holder 
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

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

2016-11-28 Thread Tsjerk Wassenaar 
Hi Thomas,

Yeah, this one catches me off-guard now and again. Chain labels were made
case-sensitive, as assemblies sometimes become so large that more than 26
labels are required. So, you'll probably need to specify 'chain A' in stead
of 'chain a'.

Hope it helps,

Tsjerk

On Mon, Nov 28, 2016 at 3:13 PM,  wrote:

> Dear Tsjerk,
>
> thank you for your reply.
>
>
>
> The very simple script
>
>
>
> bg_color white
>
> load 2j6o-coot-0.pdb
>
>
>
> works fine as the pdb-file is loaded and displayed as line model (as it
> should) with v.1.8.40.
>
>
>
> Adding the line
>
>
>
> select SH3, resi 2-58 and chain a
>
>
>
> yields  a selection called SH3 (as expected) but this does not contain any
> atoms. As I already wrote, the same script (plus lots of additional lines)
> works flawlessly using v1.8.07.
>
>
>
> I will be happy about any possibly helpful suggestion.
>
>
>
> Best
>
> Thomas
>
>
>
>
>
>
>
> *Von:* Tsjerk Wassenaar [mailto:tsje...@gmail.com]
> *Gesendet:* Donnerstag, 24. November 2016 15:36
> *An:* Reubold, Thomas Dr.
> *Cc:* pymol-users
> *Betreff:* Re: [PyMOL] Scripts don't work any longer after upgrade to
> v1.8.4
>
>
>
> Hi Thomas,
>
>
>
> Can you give more information? What is in the script? Is something written
> in the terminal?
>
> FWIW, I have not encountered problems, and certainly not with selections.
> My guess is that the script breaks before getting to the selection.
>
>
>
> Cheers,
>
>
>
> Tsjerk
>
>
>
> On Thu, Nov 24, 2016 at 2:13 PM,  wrote:
>
> Hello all,
>
>
>
> after installation of Pymol v.1.8.4 on our Linux system, scripts that used
> to work fine with v.1.8.0.7 do not work anymore. Even a simple selection
> does not work.
>
> Is this a known problem? If so, is there a way to fix it?
>
> Any help is greatly appreciated.
>
>
>
> Best,
>
> Thomas
>
>
> 
> --
>
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>



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

2016-11-28 Thread Rui Sousa 
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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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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[PyMOL] PDB Format not correct for use in CHARMM

2016-11-28 Thread Marko Sever 
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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