pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all,
I was wondering if there is an option to export both the .obj and .mtl file from pymol.
Saving as .obj works perfectly fine, however when I save as .mtl the file is empty.

Am I doing something wrong here?
I saved via command line „save filename.mtl“

Would there be another option that the mtl-file is generated automatically during saving as .obj.

Thanks in advance for the help!

Verena

CLASSIFICATION: UNCLASSIFIED

Hello,

While googling for "zspace molecular visualization", I came across
http://zspace.com/about/press-releases/zspace-announces-platform-support-for
-pymol-and-avogadro released back in 2013. However, when I tried to google
for information on how to run either PyMOL or Avogadro on zSpace, I am not
able to find anything useful. 

Is the support for zSpace in PyMOL not available in the open source version?
If it is supported, where can I find more information on getting that setup?


Any pointers in greatly appreciated.... Thank you....

thanks
-simon


CLASSIFICATION: UNCLASSIFIED

Not sure why the compilers don't complain on Linux, but the mingw 
compiler demands this cast or it throws an error:


--- layer1/P.cpp.orig   2017-10-24 16:34:00 -0700
+++ layer1/P.cpp        2017-10-24 16:34:47 -0700
@@ -1782,7 +1782,7 @@
            si.wShowWindow = SW_HIDE;

            if(IsSecurityRequired()) {
-            lpSD = GlobalAlloc(GPTR, SECURITY_DESCRIPTOR_MIN_LENGTH);
+            lpSD = (PSECURITY_DESCRIPTOR) GlobalAlloc(GPTR, 
SECURITY_DESCRIPTOR_MIN_LENGTH);
              InitializeSecurityDescriptor(lpSD, 
SECURITY_DESCRIPTOR_REVISION);
              SetSecurityDescriptorDacl(lpSD, -1, 0, 0);


Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

On 23-Oct-2017 23:19, Thomas Holder wrote:
> drand48() returns a float in [0,1) whereas rand() returns an integer
> in [0,MAX_RAND].

The usual trick (this comes up frequently on mingw) is to replace 
drand48 with

(rand() / (RAND_MAX + 1.0))


Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

Hi David,

ply_c.h is part of the VMD molfile plugins.
Would the following patch fix it for you?

--- a/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h
+++ b/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h
@@ -3121,7 +3121,7 @@ void *get_new_props_ply(PlyFile *ply)
   }
 
   /* in case we need a random choice */
-#if defined(_MSC_VER)
+#ifndef _XOPEN_SOURCE
   random_pick = 0;
 #else
   random_pick = (int) floor (rules->nprops * drand48());

If this works for you, I will also suggest this change upstream to the VMD authors.

drand48() returns a float in [0,1) whereas rand() returns an integer in [0,MAX_RAND].

Cheers,
  Thomas

> On Oct 24, 2017, at 2:08 AM, mathog <ma...@ca...> wrote:
> 
> Trying to build in mingw (have done this a couple of times before).
> 
> Somebody introduced a file ply_c.h which references drand48() since the last time this was built.  That function isn't found in mingw, at least not with the compile line setup.py produced.  I can patch around this but wonder why drand48() was used instead of rand() in the first place.
> 
> Thanks,
> 
> David Mathog
> ma...@ca...
> Manager, Sequence Analysis Facility, Biology Division, Caltech

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Trying to build in mingw (have done this a couple of times before).

Somebody introduced a file ply_c.h which references drand48() since the 
last time this was built.  That function isn't found in mingw, at least 
not with the compile line setup.py produced.  I can patch around this 
but wonder why drand48() was used instead of rand() in the first place.

Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

Hi David,

Thanks for pointing out that the splash screen is out of date, we will fix that of course.

Everything else says 1.9.0.0, that is the SVN log, the ChangeLog file, the "get_version" command (given a clean build), etc.

Like Michael already pointed out, the PyMOL 2.0 announcement also announced that the 2.0 features (Qt interface etc.) will be released to Open-Source next year. The recent core feature updates (API changes, settings, bug fixes) have already been released to Open-Source, that's why we incremented the version to 1.9. Hope this makes sense to you.

Thanks also for pointing out the glitch with searching for msgpack/version_master.h, looks like we're not catching all possible exceptions there. Will fix that too. The setup.py script searches the environment variable PREFIX_PATH for headers and libraries, so if you have stuff in /usr/local, then you could export something like PREFIX_PATH=/usr/local:/usr before running setup.py.

Cheers,
  Thomas

> On Oct 20, 2017, at 10:26 PM, mathog <ma...@ca...> wrote:
> 
> On 20-Oct-2017 12:54, Michael Banck wrote:
>> Hi,
>> On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote:
>>> Pymol 2.0 was recently announced
>> That announcement was misleading, while the subject indeed said that,
>> what was actually announced was the proprietary Pymol *incentive* 2.0
>> release.
>> The open source 2.0 release is apparently pushed back to early next
>> year, this was also mentioned in the announcement.
> 
> OK, that solves one part of the puzzle.  What about the conflicting version numbers displayed by the SVN release (1.8.x vs. 1.9.0.0)?  Doesn't svn automatically increment its "revision number", or whatever it is called in that system, when each patch is applied?  I did not notice any numbers like that, not even in the "about" display, which shows "1.9.0.0".
> 
> Thanks,
> 
> David Mathog
> ma...@ca...
> Manager, Sequence Analysis Facility, Biology Division, Caltech

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

On 20-Oct-2017 12:54, Michael Banck wrote:
> Hi,
> 
> On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote:
>> Pymol 2.0 was recently announced
> 
> That announcement was misleading, while the subject indeed said that,
> what was actually announced was the proprietary Pymol *incentive* 2.0
> release.
> 
> The open source 2.0 release is apparently pushed back to early next
> year, this was also mentioned in the announcement.

OK, that solves one part of the puzzle.  What about the conflicting 
version numbers displayed by the SVN release (1.8.x vs. 1.9.0.0)?  
Doesn't svn automatically increment its "revision number", or whatever 
it is called in that system, when each patch is applied?  I did not 
notice any numbers like that, not even in the "about" display, which 
shows "1.9.0.0".

Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

Hi,

On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote:
> Pymol 2.0 was recently announced

That announcement was misleading, while the subject indeed said that,
what was actually announced was the proprietary Pymol *incentive* 2.0
release.

The open source 2.0 release is apparently pushed back to early next
year, this was also mentioned in the announcement.


Michael

Hi all,

Pymol 2.0 was recently announced and since I had not built one from 
scratch in a long time I thought I would do so to see how the process 
had changed.  Downloaded source from:

   svn://svn.code.sf.net.p/p/pymol/code/trunk/pymol

and built it.  There was a little problem with "msgpack" on Ubuntu, 
where the OS package was too old, eventually having to install that from 
source and modify setup.py like this:

<         f = os.path.join(prefix, 'local', 'include', 'msgpack', 
'version_master.h')
---
>         f = os.path.join(prefix, 'include', 'msgpack', 
> 'version_master.h')

so that it could find the local build.  Then Pymol built and installed.  
However, what version is it???

The text when it starts says

  PyMOL(TM) Molecular Graphics System, Version 1.9.0.0.

the splash screen says

  Open Source Pymol 1.8.x

I was actually expecting 2.0, given the release announcement.

Can somebody please clarify the situation?

Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

Hi Rohan,

The short answer is: You are using Python 3.

The crash issue has been reported last week and we've found the cause, I will push the fix to the SVN repo later today.

Regarding session files: This is tricky. PyMOL session files are Python pickle containers, and fundamental type changes between Python 2 and 3 make Python 3 pickles largely incompatible with Python 2. What we can handle so far:

- loading old session files into Python 3 builds
- limited support for loading Python 3 session files into new builds with Python 2

We can add a warning message if pse_export_version is used with a Python 3 build of PyMOL, because that's currently unsupported (given that all older versions use Python 2).

Cheers,
  Thomas

> On Oct 18, 2017, at 5:07 PM, Rohan Eapen <rs...@ca...> wrote:
> 
> Dear all,
> 
> I am currently using PyMOL 1.8.7.0 and have noticed a couple of issues, which I have been unable to solve so far. 
> 
> If I highlight over the "copy to object" line on the action bar in PyMOL viewer it crashes the program. This occurs on both selections and objects. I have attempted to work my way through the source code, and see nothing immediately in fault comparing it to codes found on https://sourceforge.net/p/pymol/code/4177/
> 
> I am also attempting to export .pse files to be compatible with earlier versions of PyMOL. I am able to save them (supposedly in their compatible forms), but no one with any earlier versions of PyMOL are able to open them. This is the error that is seen when attempting to open the .pse file.
> 
> Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 1.30.
>  OpenGL graphics engine:
>   GL_VENDOR:   Intel Open Source Technology Center
>   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile 
>   GL_VERSION:  3.0 Mesa 17.0.7
>  Adjusting settings to improve performance for Intel cards.
>  Detected 4 CPU cores.  Enabled multithreaded rendering.
> 
> Warning: This session was created with a newer version of PyMOL (1.870).
> Warning: Some content may not load completely.
> ExectiveSetSession-Error: after settings.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
>  Executive: skipping unrecognized object "" of type 0.
> ExectiveSetSession-Error: after names.
> ExectiveSetSession-Warning: restore may be incomplete.
> 
> 
> Any help would be greatly appreciated!
> 
> Many thanks,
> Rohan
> -- 
> Rohan Eapen
> Itzhaki group - PhD student
> Department of Pharmacology
> University of Cambridge
> Tennis Court Road
> CB2 1PD
> rs...@ca...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear all,

I am currently using PyMOL 1.8.7.0 and have noticed a couple of issues,
which I have been unable to solve so far.

If I highlight over the "copy to object" line on the action bar in PyMOL
viewer it crashes the program. This occurs on both selections and objects.
I have attempted to work my way through the source code, and see nothing
immediately in fault comparing it to codes found on
https://sourceforge.net/p/pymol/code/4177/

I am also attempting to export .pse files to be compatible with earlier
versions of PyMOL. I am able to save them (supposedly in their compatible
forms), but no one with any earlier versions of PyMOL are able to open
them. This is the error that is seen when attempting to open the .pse file.

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   Intel Open Source Technology Center
  GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
  GL_VERSION:  3.0 Mesa 17.0.7
 Adjusting settings to improve performance for Intel cards.
 Detected 4 CPU cores.  Enabled multithreaded rendering.

Warning: This session was created with a newer version of PyMOL (1.870).
Warning: Some content may not load completely.
ExectiveSetSession-Error: after settings.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
 Executive: skipping unrecognized object "" of type 0.
ExectiveSetSession-Error: after names.
ExectiveSetSession-Warning: restore may be incomplete.


Any help would be greatly appreciated!

Many thanks,
Rohan
-- 
Rohan Eapen
Itzhaki group - PhD student
Department of Pharmacology
University of Cambridge
Tennis Court Road
CB2 1PD
rs...@ca...

nevermind, I was entering @distance.py instead of run distance.py

On Fri, Oct 13, 2017 at 2:05 PM, Leigh M <lei...@gm...> wrote:

> Hi Jared-
>
> I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 +
> dy**2 + dz**2).
> I've been using python alone without pymol...using your code with the
> pymol api works for individual distances but I'm calculating hundreds of
> distances and need to write to a csv which does not seem to be working.
> I get an error:  NameError: name 'csvfile' is not defined
>
> for k,v in AA_dict.items():
>     vA = v[0:3]
>     for k2, v2 in AA_dict.items():
>         vA2 = v2[0:3]
>         point1 = '/5p21//A/'+ vA2 + '`' + str(k2) + '/CA'
>         point2 = '/5p21//A/' + vA + '`' + str(k) + '/CA'
>         o = cmd.get_coords(point1)[0]
>         h = cmd.get_coords(point2)[0]
>         dx = h[0] - o[0]
>         dy = h[1] - o[1]
>         dz = h[2] - o[2]
>         d = math.sqrt(dx ** 2 + dy ** 2 + dz ** 2)
>         dist_dict[(v, v2)] = d
>
> with open(protein + '_distances.csv', 'w') as csvfile:
>     fieldnames = dist_dict.keys()
>     writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
>     writer.writeheader()
>     writer.writerow(dist_dict)  # writes the chi angles
>     csvfile.close()
>
>
> Thanks
>
> Leigh
>
> On Thu, Oct 12, 2017 at 8:44 PM, Jared Sampson <jar...@co...
> > wrote:
>
>> Hi Leigh -
>>
>> How are you getting the coordinates?  This works for me:
>>
>> ```
>> import math
>>
>> # Show more digits for the distance label
>> set label_distance_digits, 10
>>
>> # Make an alanine residue
>> fab A, ala
>>
>> # Get coordinates from 2 atoms
>> o = cmd.get_coords("/ala///1/O")[0]
>> h = cmd.get_coords("/ala///1/H")[0]
>>
>> # Calculate the distance
>> dx = h[0] - o[0]
>> dy = h[1] - o[1]
>> dz = h[2] - o[2]
>> d = math.sqrt(dx**2 + dy**2 + dz**2)
>> print(d)
>>
>> # Distance from script: 2.3546268062493567
>> # Distance from wizard: 2.354626655  (label maxes out at 10 digits)
>> ```
>>
>> Those values seem close enough to me.  Is it possible that in your script
>> you're getting the coordinates for the i+1 or i-1 atom instead, or a
>> different state?  Or maybe picking the other side of a symmetric side chain
>> (e.g. OD1 vs OD2)?  If you could share the relevant portion of the script,
>> you might get some more useful feedback; right now all we can do is guess!
>>
>> Cheers,
>> Jared
>>
>>
>> On October 12, 2017 at 2:19:36 PM, Leigh M (lei...@gm...)
>> wrote:
>>
>> Anyone know how pymol calculates distance between two atoms?
>> I wrote a python script that calculates distance using the distance
>> formula and the xyz coordinates in the pdb, and it differs from the wizard
>> by ~40%. Any ideas on what might be going on would be helpdul
>>
>> Thanks!
>>
>> Leigh
>> ------------------------------------------------------------------------------
>>
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>

Hi Jared-

I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 + dy**2
+ dz**2).
I've been using python alone without pymol...using your code with the pymol
api works for individual distances but I'm calculating hundreds of
distances and need to write to a csv which does not seem to be working.
I get an error:  NameError: name 'csvfile' is not defined

for k,v in AA_dict.items():
    vA = v[0:3]
    for k2, v2 in AA_dict.items():
        vA2 = v2[0:3]
        point1 = '/5p21//A/'+ vA2 + '`' + str(k2) + '/CA'
        point2 = '/5p21//A/' + vA + '`' + str(k) + '/CA'
        o = cmd.get_coords(point1)[0]
        h = cmd.get_coords(point2)[0]
        dx = h[0] - o[0]
        dy = h[1] - o[1]
        dz = h[2] - o[2]
        d = math.sqrt(dx ** 2 + dy ** 2 + dz ** 2)
        dist_dict[(v, v2)] = d

with open(protein + '_distances.csv', 'w') as csvfile:
    fieldnames = dist_dict.keys()
    writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
    writer.writeheader()
    writer.writerow(dist_dict)  # writes the chi angles
    csvfile.close()


Thanks

Leigh

On Thu, Oct 12, 2017 at 8:44 PM, Jared Sampson <jar...@co...>
wrote:

> Hi Leigh -
>
> How are you getting the coordinates?  This works for me:
>
> ```
> import math
>
> # Show more digits for the distance label
> set label_distance_digits, 10
>
> # Make an alanine residue
> fab A, ala
>
> # Get coordinates from 2 atoms
> o = cmd.get_coords("/ala///1/O")[0]
> h = cmd.get_coords("/ala///1/H")[0]
>
> # Calculate the distance
> dx = h[0] - o[0]
> dy = h[1] - o[1]
> dz = h[2] - o[2]
> d = math.sqrt(dx**2 + dy**2 + dz**2)
> print(d)
>
> # Distance from script: 2.3546268062493567
> # Distance from wizard: 2.354626655  (label maxes out at 10 digits)
> ```
>
> Those values seem close enough to me.  Is it possible that in your script
> you're getting the coordinates for the i+1 or i-1 atom instead, or a
> different state?  Or maybe picking the other side of a symmetric side chain
> (e.g. OD1 vs OD2)?  If you could share the relevant portion of the script,
> you might get some more useful feedback; right now all we can do is guess!
>
> Cheers,
> Jared
>
>
> On October 12, 2017 at 2:19:36 PM, Leigh M (lei...@gm...)
> wrote:
>
> Anyone know how pymol calculates distance between two atoms?
> I wrote a python script that calculates distance using the distance
> formula and the xyz coordinates in the pdb, and it differs from the wizard
> by ~40%. Any ideas on what might be going on would be helpdul
>
> Thanks!
>
> Leigh
> ------------------------------------------------------------------------------
>
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> _________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>

Hi Leigh - 

How are you getting the coordinates?  This works for me:

```
import math

# Show more digits for the distance label
set label_distance_digits, 10

# Make an alanine residue
fab A, ala

# Get coordinates from 2 atoms
o = cmd.get_coords("/ala///1/O")[0]
h = cmd.get_coords("/ala///1/H")[0]

# Calculate the distance
dx = h[0] - o[0]
dy = h[1] - o[1]
dz = h[2] - o[2]
d = math.sqrt(dx**2 + dy**2 + dz**2)
print(d)

# Distance from script: 2.3546268062493567
# Distance from wizard: 2.354626655  (label maxes out at 10 digits)
```

Those values seem close enough to me.  Is it possible that in your script you're getting the coordinates for the i+1 or i-1 atom instead, or a different state?  Or maybe picking the other side of a symmetric side chain (e.g. OD1 vs OD2)?  If you could share the relevant portion of the script, you might get some more useful feedback; right now all we can do is guess!

Cheers,
Jared


On October 12, 2017 at 2:19:36 PM, Leigh M (lei...@gm...) wrote:

Anyone know how pymol calculates distance between two atoms? 
I wrote a python script that calculates distance using the distance formula and the xyz coordinates in the pdb, and it differs from the wizard by ~40%. Any ideas on what might be going on would be helpdul

Thanks!

Leigh
------------------------------------------------------------------------------  
Check out the vibrant tech community on one of the world's most  
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________  
PyMOL-users mailing list (PyM...@li...)  
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users  
Archives: http://www.mail-archive.com/pym...@li...

yep!

On Thu, Oct 12, 2017 at 2:07 PM, Roger Rowlett <rro...@co...> wrote:

> You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1,
> etc.)
>
> _______________________________________
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245 <(315)%20228-7245>
> ofc: (315)-228-7395 <(315)%20228-7395>
> fax: (315)-228-7935 <(315)%20228-7935>
> email: rro...@co...
>
>
> On 10/12/2017 2:18 PM, Leigh M wrote:
>
> Anyone know how pymol calculates distance between two atoms?
> I wrote a python script that calculates distance using the distance
> formula and the xyz coordinates in the pdb, and it differs from the wizard
> by ~40%. Any ideas on what might be going on would be helpdul
>
> Thanks!
>
> Leigh
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1, 
etc.)

_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@co...

On 10/12/2017 2:18 PM, Leigh M wrote:
> Anyone know how pymol calculates distance between two atoms?
> I wrote a python script that calculates distance using the distance 
> formula and the xyz coordinates in the pdb, and it differs from the 
> wizard by ~40%. Any ideas on what might be going on would be helpdul
>
> Thanks!
>
> Leigh
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Anyone know how pymol calculates distance between two atoms?
I wrote a python script that calculates distance using the distance formula
and the xyz coordinates in the pdb, and it differs from the wizard by ~40%.
Any ideas on what might be going on would be helpdul

Thanks!

Leigh

<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=utf-8">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <br>
    <div class="moz-forward-container"><br>
      <meta http-equiv="content-type" content="text/html; charset=utf-8">
      <p><tt>Hello, <br>
        </tt></p>
      <p>any idea what could be wrong when Pymol graphics are too big
        for the actual window. See attached. Everything seems zoomed out
        and part of the menus, sequence etc are not visible in the
        window. But mouse responds to correct position of where the menu
        items are, ca. half a menu height below what I see. Can I fix
        this somehow or should I just reinstall? It happened all of a
        sudden and suspect will happen again, so hoping for a fix...
        Everything else is ok, including the Pymol Tcl/Tk command
        window. Looks like PyMol is thinking my screen resolution/window
        size is something different from what it
        really is...<br>
      </p>
      <p>This is version 1.8.2 on Win10 laptop with 4k resolution
        monitor and GeForce graphics. <br>
      </p>
      <p>cheers, Marko<br>
      </p>
      <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

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Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

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Hi Marko,

We have seen this issue with Intel HD graphics, but not with Nvidia. Any chance this is a dual graphics machine and you're actually not using the Nvidia chip?

Anyway, for Intel graphics there are several options to resolve it:

1) Upgrade to PyMOL 2.0 (recommended)

2) and/or switch to Nvidia chip in case this is dual graphics setup

3) or downgrade the Intel graphics driver

Cheers,
  Thomas

> On Oct 9, 2017, at 1:02 PM, Marko Hyvonen <mh...@ca...> wrote:
> 
> Hello, 
> 
> any idea what could be wrong when Pymol graphics are too big for the actual window. See attached. Everything seems zoomed out and part of the menus, sequence etc are not visible in the window. But mouse responds to correct position of where the menu items are, ca. half a menu height below what I see. Can I fix this somehow or should I just reinstall? It happened all of a sudden and suspect will happen again, so hoping for a fix... Everything else is ok, including the Pymol Tcl/Tk command window. Looks like PyMol is thinking my screen resolution is something different from what it is...
> This is version 1.8.2 on Win10 with 4k resolution monitor and GeForce graphics. 
> cheers, Marko
> -- 
> 
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> 
> mh...@ca...
> 
> +44 (0)1223 766 044
> @HyvonenGroup
> 
> http://hyvonen.bioc.cam.ac.uk
> 
> <PyMol_screen.jpg>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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    <p><tt>Hello, <br>
      </tt></p>
    <p>any idea what could be wrong when Pymol graphics are too big for
      the actual window. See attached. Everything seems zoomed out and
      part of the menus, sequence etc are not visible in the window. But
      mouse responds to correct position of where the menu items are,
      ca. half a menu height below what I see. Can I fix this somehow or
      should I just reinstall? It happened all of a sudden and suspect
      will happen again, so hoping for a fix... Everything else is ok,
      including the Pymol Tcl/Tk command window. Looks like PyMol is
      thinking my screen resolution is something different from what it
      is...<br>
    </p>
    <p>This is version 1.8.2 on Win10 with 4k resolution monitor and
      GeForce graphics. <br>
    </p>
    <p>cheers, Marko<br>
    </p>
    <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

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Clarification: valence_size for sticks does not work. It does work for 
lines.


On 10/03/2017 04:32 PM, Paul Paukstelis wrote:
> I cannot seem to get the "valence_size" setting to do anything. 
> Regardless of the setting, double bonds are drawn the same distance 
> apart. Bug or am I missing something? (Pymol. 2.0 incentive).
>

I cannot seem to get the "valence_size" setting to do anything. 
Regardless of the setting, double bonds are drawn the same distance 
apart. Bug or am I missing something? (Pymol. 2.0 incentive).