Thanks, all. Looks like I'll have to investigate local issues with our
institutional firewall. Sigh. Not the first time...
Roger Rowlett
On Mar 22, 2011 12:58 PM, "Jason Vertrees"
wrote:
> Great, thanks, David. Just ensuring the problems been isolated.
>
> Cheers,
>
> -- Jason
>
> On Tue, Mar 22
Hi Roger,
Just to clarify, for the FTP protocol the correct prefix is
ftp://ftp.wwpdb.org/
and NOT
http://ftp ...
Hope that makes sense,
Andreas
On Tue, Mar 22, 2011 at 9:54 AM, Jason Vertrees
wrote:
> Great, thanks, David. Just ensuring the problems been isolated.
>
> Cheers,
>
> -- Jaso
Resolves fine for me.
-David
On Mar 22, 2011, at 12:30 PM, Jason Vertrees
wrote:
> Hi Roger,
>
> On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote:
>> Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it
>> is currently generating a "cannot be found" error". I'll i
Great, thanks, David. Just ensuring the problems been isolated.
Cheers,
-- Jason
On Tue, Mar 22, 2011 at 9:53 AM, David Hall wrote:
> Resolves fine for me.
>
> -David
>
> On Mar 22, 2011, at 12:30 PM, Jason Vertrees
> wrote:
>
>> Hi Roger,
>>
>> On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett
Hi Roger,
On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote:
> Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it
> is currently generating a "cannot be found" error". I'll investigate
> further. This may be the issue with pymol if it is using that server path.
This
Hi Jason,
Can you clarify what URL is being used to download the files from RCSB
PDB? I don't think that there was any change regarding those last
year.
Andreas
On Tue, Mar 22, 2011 at 9:02 AM, Jason Vertrees
wrote:
> Hi Roger,
>
>> Has anyone else noticed that Pymol (v 1.3 or 1.4) will no lon
Hi Roger,
> Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data
> from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK,
> but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession
> number.
I just checked v1.4 and I'm not having any
Has anyone else noticed that Pymol (v 1.3 or
1.4) will no longer fetch data from the pdb server? If I issue
'set fetch_host, pdbe' I can fetch data OK, but if you 'set
fetch_host, pdb' I'm getting a fetch error for any accession
number.
--
Hi Virasak,
In Pymol you can change the element type to match your needs:
alter n. si, elem="si"
Hope it helps,
Tsjerk
On Tue, Mar 22, 2011 at 2:44 PM, Virasak Dungsrikaew wrote:
> Hi Tsjerk,
>
> You are right. In my work, I almost working with XYZ format and all
> programs that I used is wor
I had the same problem.
Email Joe Dundas for the .py source code .py file,
and drop it into the modules/pmg_tk/startup folder.
Jed
Hongbo Zhu wrote:
> Hi, Tomas,
> Usually, the "Bad magic number" is caused by wrong python version when
> running .pyc file (the .pyc must have been compiled using
Hi Virasak,
It goes a bit far to call it a bug. It's a problem with the xyz
format. It only has names for atoms, not element types, and Pymol
can't go guessing, otherwise any CA would end up as calcium :S
Cheers,
Tsjerk
On Tue, Mar 22, 2011 at 2:30 PM, Virasak Dungsrikaew wrote:
> Hi Tsjerk,
>
Hi Kanika,
They should. The CRYST1 record holds all the information required to
build the crystal. Do note that the symexp command generates
neighbouring symmetry mates, given a cut off distance. It does not
build the filled unit cell. Thomas put a script on the wiki last year
to build you that: h
You are right, Thomas! The information is redundant in REMARK 290.
I just performed a small test which confirms your conclusion:
remove CRYST1 will make symexp to complain "ExecutiveSymExp-Error: No
symmetry loaded!" even if REMARK 290 is present, while removing REMARK
290 does not have any effe
Should not the positions of ASU's generated by REMARK290 be same as the
symmetry mates generated?
--
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of y
Dear all,
I am using PyMOL 1.2r2 on Ubuntu 10.10.
When I click 'Save Molecule...' from 'File' menu and select a molecule
that contained 'Si' atom, the output pdb will show 'S' instead of 'Si'
on the right most column.
I also try this with mol format, the result is the same.
Is this a known bug or
> It seems REMARK 290 that contains crystallographic symmetry
> transformations is used for computing the positions of neighboring ASUs.
the CRYST1 record is sufficient for generating symmetry mates, so
pymol most likely does not read REMARK 290.
Cheers,
Thomas
--
Thomas Holder
MPI for Develo
Hi, Tomas,
Usually, the "Bad magic number" is caused by wrong python version when
running .pyc file (the .pyc must have been compiled using a different
version of python than the one in PyMOL 1.3, which is python 2.5.4).
Maybe you have also noticed on the first line of the CASTpyMOL webpage :
"
Hello pymol users,
I try to install this castp plugin:
http://sts.bioengr.uic.edu/castp/pymol.php
-> http://sts.bioengr.uic.edu/castp/infoPages/CASTpyMOL_v2.pyc
I have pymol 1.3 (windows7 64bit)
and I got:
ImportError: Bad magic number in C:\Program Files
(x86)\PyMOL\PyMOL/modules\pmg_tk\startu
El 22/03/11 09:34, Justin Lecher escribió:
> On 21/03/11 22:57, Hongbo Zhu wrote:
>> Dear PyMOLers,
>>
>> As many of you might be aware of, MSMS is an excellent program developed
>> by Michel Sanner for computing protein surface, especially solvent
>> excluded surface (SES). (see http://mgltools.
Hi, Kanika,
The source code can be found at function
ExecutiveSymExp()
in the file
./trunk/pymol/layer3/Executive.c
Normally, a PDB is equivalent to an ASU (except for some cases like
capsid). "Symexp is used to reconstruct neighboring ASUs."
( http://pymolwiki.org/index.php/Symexp )
It seems RE
On 21/03/11 22:57, Hongbo Zhu wrote:
> Dear PyMOLers,
>
> As many of you might be aware of, MSMS is an excellent program developed
> by Michel Sanner for computing protein surface, especially solvent
> excluded surface (SES). (see http://mgltools.scripps.edu/packages/MSMS/
> ). Due to its outst
I'll be at ACS! See you and the developers there.
Paul
--
Paul Rigor
http://www.ics.uci.edu/~prigor
On Tue, Mar 22, 2011 at 12:09 AM, Jason Vertrees
wrote:
> Hi all,
>
> Just a quick note to let you know that PyMOL will be represented at
> the Schrodinger booths at the WCPCW in Monterey, CA (
Hi all,
Just a quick note to let you know that PyMOL will be represented at
the Schrodinger booths at the WCPCW in Monterey, CA (this week) and
ACS in Anaheim (next week). So, if you're at either meeting, please
feel free to stop by and come talk PyMOL, ask questions, or just chat.
Cheers,
-- J
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