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,
--
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
jason.vertr...@schrodinger.com wrote:
Hi all,
Just a quick note to let you know that PyMOL will be represented at
the Schrodinger booths at
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
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
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
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
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 :
To
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
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
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
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
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:
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 vira...@gmail.com
I had the same problem.
Email Joe Dundas jdunda1 at gmail 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
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 vira...@gmail.com wrote:
Hi Tsjerk,
You are right. In my work, I almost working with XYZ format and all
programs that I
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 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
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
jason.vertr...@schrodinger.com wrote:
Hi Roger,
Has anyone else noticed that Pymol
Hi Roger,
On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu 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
Great, thanks, David. Just ensuring the problems been isolated.
Cheers,
-- Jason
On Tue, Mar 22, 2011 at 9:53 AM, David Hall li...@cowsandmilk.net wrote:
Resolves fine for me.
-David
On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com
wrote:
Hi Roger,
On Tue,
Resolves fine for me.
-David
On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com
wrote:
Hi Roger,
On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu wrote:
Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it
is currently
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
jason.vertr...@schrodinger.com wrote:
Great, thanks, David. Just ensuring the problems been
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 jason.vertr...@schrodinger.com
wrote:
Great, thanks, David. Just ensuring the problems been isolated.
Cheers,
--
23 matches
Mail list logo